From 8649403cc964981e28e34386d1624828de919f69 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Mon, 25 Nov 2024 14:32:27 +0100 Subject: [PATCH] add linter skip rules for 24.2 --- .../data_manager_dram_database_downloader/.lint_skip | 1 + .../.lint_skip | 1 + data_managers/data_manager_fetch_refseq/.lint_skip | 1 + .../.lint_skip | 1 + data_managers/data_manager_interproscan/.lint_skip | 1 + .../data_manager_malt_index_builder/.lint_skip | 1 + .../data_manager_mapseq/data_manager/.lint_skip | 1 + .../data_manager_mash_sketch_builder/.lint_skip | 1 + data_managers/data_manager_pangolin_data/.lint_skip | 1 + .../data_manager_pharokka_database_fetcher/.lint_skip | 1 + .../data_manager_primer_scheme_bedfiles/.lint_skip | 1 + .../data_manager_selection_background/.lint_skip | 1 + data_managers/data_manager_snpsift_dbnsfp/.lint_skip | 1 + tool_collections/bamtools/bamtools/.lint_skip | 1 + tool_collections/bamtools/bamtools_filter/.lint_skip | 1 + tool_collections/biotradis/.lint_skip | 1 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tools/ncbi_entrez_eutils/.lint_skip create mode 100644 tools/ncbi_fcs_gx/.lint_skip create mode 100644 tools/nonpareil/.lint_skip create mode 100644 tools/novoplasty/.lint_skip create mode 100644 tools/obitools/.lint_skip create mode 100644 tools/orthofinder/.lint_skip create mode 100644 tools/pangolin/.lint_skip create mode 100644 tools/pbmm2/.lint_skip create mode 100644 tools/pbtk/.lint_skip create mode 100644 tools/peakzilla/.lint_skip create mode 100644 tools/phyml/.lint_skip create mode 100644 tools/picrust/.lint_skip create mode 100644 tools/plasmidfinder/.lint_skip create mode 100644 tools/polypolish/.lint_skip create mode 100644 tools/porechop/.lint_skip create mode 100644 tools/pretext/.lint_skip create mode 100644 tools/prot-scriber/.lint_skip create mode 100644 tools/proteinortho/.lint_skip create mode 100644 tools/purge_dups/.lint_skip create mode 100644 tools/pyega3/.lint_skip create mode 100644 tools/pygenometracks/.lint_skip create mode 100644 tools/pysradb/.lint_skip create mode 100644 tools/qfilt/.lint_skip create mode 100644 tools/quast/.lint_skip create mode 100644 tools/query_impc/.lint_skip create mode 100644 tools/query_tabular/.lint_skip create mode 100644 tools/quickmerge/.lint_skip create mode 100644 tools/rasusa/.lint_skip create mode 100644 tools/raxml/.lint_skip create mode 100644 tools/read_it_and_keep/.lint_skip create mode 100644 tools/recentrifuge/.lint_skip create mode 100644 tools/revoluzer/.lint_skip create mode 100644 tools/rgrnastar/.lint_skip create mode 100644 tools/rnaquast/.lint_skip create mode 100644 tools/rpbasicdesign/.lint_skip create mode 100644 tools/rseqc/.lint_skip create mode 100644 tools/scanpy/.lint_skip create mode 100644 tools/sceasy/.lint_skip create mode 100644 tools/scoary/.lint_skip create mode 100644 tools/seacr/.lint_skip create mode 100644 tools/semibin/.lint_skip create mode 100644 tools/seqkit/.lint_skip create mode 100644 tools/seqprep/.lint_skip create mode 100644 tools/seqsero2/.lint_skip create mode 100644 tools/seqtk/.lint_skip create mode 100644 tools/seurat/.lint_skip create mode 100644 tools/shasta/.lint_skip create mode 100644 tools/shovill/.lint_skip create mode 100644 tools/sinto/.lint_skip create mode 100644 tools/sleuth/.lint_skip create mode 100644 tools/smudgeplot/.lint_skip create mode 100644 tools/snapatac2/.lint_skip create mode 100644 tools/sniffles/.lint_skip create mode 100644 tools/snipit/.lint_skip create mode 100644 tools/snp-sites/.lint_skip create mode 100644 tools/sonneityping/.lint_skip create mode 100644 tools/spades/.lint_skip create mode 100644 tools/spapros/.lint_skip create mode 100644 tools/sra-tools/.lint_skip create mode 100644 tools/straindesign/.lint_skip create mode 100644 tools/stringtie/.lint_skip create mode 100644 tools/taxonomy_filter_refseq/.lint_skip create mode 100644 tools/taxonomy_krona_chart/.lint_skip create mode 100644 tools/tb-profiler/.lint_skip create mode 100644 tools/te_finder/.lint_skip create mode 100644 tools/tooldistillator/.lint_skip create mode 100644 tools/tracegroomer/.lint_skip create mode 100644 tools/transtermhp/.lint_skip create mode 100644 tools/trimal/.lint_skip create mode 100644 tools/trimmomatic/.lint_skip create mode 100644 tools/trinity/.lint_skip create mode 100644 tools/trycycler/.lint_skip create mode 100644 tools/ucsc_tools/fasplit/.lint_skip create mode 100644 tools/ucsc_tools/maftoaxt/.lint_skip create mode 100644 tools/umi_tools/.lint_skip create mode 100644 tools/unicycler/.lint_skip create mode 100644 tools/usher/.lint_skip create mode 100644 tools/varvamp/.lint_skip create mode 100644 tools/vcf2maf/.lint_skip create mode 100644 tools/vegan/.lint_skip create mode 100644 tools/verkko/.lint_skip create mode 100644 tools/virheat/.lint_skip create mode 100644 tools/volcanoplot/.lint_skip create mode 100644 tools/vsnp/.lint_skip create mode 100644 tools/weblogo3/.lint_skip create mode 100644 tools/windowmasker/.lint_skip create mode 100644 tools/yahs/.lint_skip diff --git a/data_managers/data_manager_dram_database_downloader/.lint_skip b/data_managers/data_manager_dram_database_downloader/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/data_managers/data_manager_dram_database_downloader/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/data_managers/data_manager_fetch_genome_dbkeys_all_fasta/.lint_skip b/data_managers/data_manager_fetch_genome_dbkeys_all_fasta/.lint_skip index 46f5e08e85b..a5aef4c7624 100644 --- a/data_managers/data_manager_fetch_genome_dbkeys_all_fasta/.lint_skip +++ b/data_managers/data_manager_fetch_genome_dbkeys_all_fasta/.lint_skip @@ -1 +1,2 @@ CitationsMissing +TestsCaseValidation diff --git a/data_managers/data_manager_fetch_refseq/.lint_skip b/data_managers/data_manager_fetch_refseq/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/data_managers/data_manager_fetch_refseq/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/data_managers/data_manager_genomic_super_signature_ravmodels/.lint_skip b/data_managers/data_manager_genomic_super_signature_ravmodels/.lint_skip index 46f5e08e85b..a5aef4c7624 100644 --- a/data_managers/data_manager_genomic_super_signature_ravmodels/.lint_skip +++ b/data_managers/data_manager_genomic_super_signature_ravmodels/.lint_skip @@ -1 +1,2 @@ CitationsMissing +TestsCaseValidation diff --git a/data_managers/data_manager_interproscan/.lint_skip b/data_managers/data_manager_interproscan/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/data_managers/data_manager_interproscan/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/data_managers/data_manager_malt_index_builder/.lint_skip b/data_managers/data_manager_malt_index_builder/.lint_skip index a68d017209e..1f78d73fa84 100644 --- a/data_managers/data_manager_malt_index_builder/.lint_skip +++ b/data_managers/data_manager_malt_index_builder/.lint_skip @@ -1 +1,2 @@ +TestsCaseValidation XMLOrder diff --git a/data_managers/data_manager_mapseq/data_manager/.lint_skip b/data_managers/data_manager_mapseq/data_manager/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/data_managers/data_manager_mapseq/data_manager/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/data_managers/data_manager_mash_sketch_builder/.lint_skip b/data_managers/data_manager_mash_sketch_builder/.lint_skip index a68d017209e..1f78d73fa84 100644 --- a/data_managers/data_manager_mash_sketch_builder/.lint_skip +++ b/data_managers/data_manager_mash_sketch_builder/.lint_skip @@ -1 +1,2 @@ +TestsCaseValidation XMLOrder diff --git a/data_managers/data_manager_pangolin_data/.lint_skip b/data_managers/data_manager_pangolin_data/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/data_managers/data_manager_pangolin_data/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/data_managers/data_manager_pharokka_database_fetcher/.lint_skip b/data_managers/data_manager_pharokka_database_fetcher/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/data_managers/data_manager_pharokka_database_fetcher/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/data_managers/data_manager_primer_scheme_bedfiles/.lint_skip b/data_managers/data_manager_primer_scheme_bedfiles/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/data_managers/data_manager_primer_scheme_bedfiles/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/data_managers/data_manager_selection_background/.lint_skip b/data_managers/data_manager_selection_background/.lint_skip index d3a1493f388..d4815fbfdaf 100644 --- a/data_managers/data_manager_selection_background/.lint_skip +++ b/data_managers/data_manager_selection_background/.lint_skip @@ -1,2 +1,3 @@ CitationsMissing HelpEmpty +TestsCaseValidation diff --git a/data_managers/data_manager_snpsift_dbnsfp/.lint_skip b/data_managers/data_manager_snpsift_dbnsfp/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/data_managers/data_manager_snpsift_dbnsfp/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tool_collections/bamtools/bamtools/.lint_skip b/tool_collections/bamtools/bamtools/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tool_collections/bamtools/bamtools/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tool_collections/bamtools/bamtools_filter/.lint_skip b/tool_collections/bamtools/bamtools_filter/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tool_collections/bamtools/bamtools_filter/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tool_collections/biotradis/.lint_skip b/tool_collections/biotradis/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tool_collections/biotradis/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tool_collections/cufflinks/cuffcompare/.lint_skip b/tool_collections/cufflinks/cuffcompare/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tool_collections/cufflinks/cuffcompare/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tool_collections/cufflinks/cuffdiff/.lint_skip b/tool_collections/cufflinks/cuffdiff/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tool_collections/cufflinks/cuffdiff/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tool_collections/cufflinks/cufflinks/.lint_skip b/tool_collections/cufflinks/cufflinks/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tool_collections/cufflinks/cufflinks/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tool_collections/cufflinks/cuffmerge/.lint_skip b/tool_collections/cufflinks/cuffmerge/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tool_collections/cufflinks/cuffmerge/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tool_collections/cufflinks/cuffquant/.lint_skip b/tool_collections/cufflinks/cuffquant/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tool_collections/cufflinks/cuffquant/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tool_collections/fastx_toolkit/fastq_quality_converter/.lint_skip b/tool_collections/fastx_toolkit/fastq_quality_converter/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastq_quality_converter/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tool_collections/fastx_toolkit/fastq_to_fasta/.lint_skip b/tool_collections/fastx_toolkit/fastq_to_fasta/.lint_skip new file mode 100644 index 00000000000..4835fb975a3 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastq_to_fasta/.lint_skip @@ -0,0 +1,2 @@ +OutputsFilterExpression +TestsCaseValidation diff --git a/tool_collections/fastx_toolkit/fastx_barcode_splitter/.lint_skip b/tool_collections/fastx_toolkit/fastx_barcode_splitter/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_barcode_splitter/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tool_collections/fastx_toolkit/fastx_clipper/.lint_skip b/tool_collections/fastx_toolkit/fastx_clipper/.lint_skip index f1a9e0e1123..8e99104d76c 100644 --- a/tool_collections/fastx_toolkit/fastx_clipper/.lint_skip +++ b/tool_collections/fastx_toolkit/fastx_clipper/.lint_skip @@ -1 +1,2 @@ InputsSelectOptionsDeprecatedAttr +TestsCaseValidation diff --git a/tool_collections/galaxy_sequence_utils/fastq_filter/.lint_skip b/tool_collections/galaxy_sequence_utils/fastq_filter/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tool_collections/galaxy_sequence_utils/fastq_filter/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tool_collections/galaxy_sequence_utils/fastq_groomer/.lint_skip b/tool_collections/galaxy_sequence_utils/fastq_groomer/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tool_collections/galaxy_sequence_utils/fastq_groomer/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tool_collections/galaxy_sequence_utils/fastq_manipulation/.lint_skip b/tool_collections/galaxy_sequence_utils/fastq_manipulation/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tool_collections/galaxy_sequence_utils/fastq_manipulation/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer/.lint_skip b/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer/.lint_skip index dd9d172c416..a8ec4fdf31f 100644 --- a/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer/.lint_skip +++ b/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer/.lint_skip @@ -1,2 +1,3 @@ # Allow duplicated labels (since filters are disjoint) -OutputsLabelDuplicatedFilter \ No newline at end of file +OutputsLabelDuplicatedFilterTestsCaseValidation +TestsCaseValidation diff --git a/tool_collections/galaxy_sequence_utils/fastq_trimmer/.lint_skip b/tool_collections/galaxy_sequence_utils/fastq_trimmer/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tool_collections/galaxy_sequence_utils/fastq_trimmer/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tool_collections/kraken/.lint_skip b/tool_collections/kraken/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tool_collections/kraken/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tool_collections/kraken2/kraken2/.lint_skip b/tool_collections/kraken2/kraken2/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tool_collections/kraken2/kraken2/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tool_collections/samtools/.lint_skip b/tool_collections/samtools/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tool_collections/samtools/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tool_collections/samtools/bam_to_cram/.lint_skip b/tool_collections/samtools/bam_to_cram/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tool_collections/samtools/bam_to_cram/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tool_collections/samtools/cram_to_bam/.lint_skip b/tool_collections/samtools/cram_to_bam/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tool_collections/samtools/cram_to_bam/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tool_collections/samtools/sam_to_bam/.lint_skip b/tool_collections/samtools/sam_to_bam/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tool_collections/samtools/sam_to_bam/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tool_collections/samtools/samtools_ampliconclip/.lint_skip b/tool_collections/samtools/samtools_ampliconclip/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tool_collections/samtools/samtools_ampliconclip/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tool_collections/samtools/samtools_bedcov/.lint_skip b/tool_collections/samtools/samtools_bedcov/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tool_collections/samtools/samtools_bedcov/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tool_collections/samtools/samtools_calmd/.lint_skip b/tool_collections/samtools/samtools_calmd/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tool_collections/samtools/samtools_calmd/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tool_collections/samtools/samtools_coverage/.lint_skip b/tool_collections/samtools/samtools_coverage/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tool_collections/samtools/samtools_coverage/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tool_collections/samtools/samtools_depth/.lint_skip b/tool_collections/samtools/samtools_depth/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tool_collections/samtools/samtools_depth/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tool_collections/samtools/samtools_fastx/.lint_skip b/tool_collections/samtools/samtools_fastx/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tool_collections/samtools/samtools_fastx/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tool_collections/samtools/samtools_fixmate/.lint_skip b/tool_collections/samtools/samtools_fixmate/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tool_collections/samtools/samtools_fixmate/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tool_collections/samtools/samtools_markdup/.lint_skip b/tool_collections/samtools/samtools_markdup/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tool_collections/samtools/samtools_markdup/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tool_collections/samtools/samtools_merge/.lint_skip b/tool_collections/samtools/samtools_merge/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tool_collections/samtools/samtools_merge/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tool_collections/samtools/samtools_mpileup/.lint_skip b/tool_collections/samtools/samtools_mpileup/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tool_collections/samtools/samtools_mpileup/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tool_collections/samtools/samtools_slice_bam/.lint_skip b/tool_collections/samtools/samtools_slice_bam/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tool_collections/samtools/samtools_slice_bam/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tool_collections/samtools/samtools_stats/.lint_skip b/tool_collections/samtools/samtools_stats/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tool_collections/samtools/samtools_stats/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tool_collections/snpeff/.lint_skip b/tool_collections/snpeff/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tool_collections/snpeff/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tool_collections/snpsift/snpsift/.lint_skip b/tool_collections/snpsift/snpsift/.lint_skip index 039bcb6e720..e54b11c9abc 100644 --- a/tool_collections/snpsift/snpsift/.lint_skip +++ b/tool_collections/snpsift/snpsift/.lint_skip @@ -1,2 +1,3 @@ +TestsCaseValidation TestsMissing XMLOrder diff --git a/tool_collections/vcflib/vcfbedintersect/.lint_skip b/tool_collections/vcflib/vcfbedintersect/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tool_collections/vcflib/vcfbedintersect/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tool_collections/vcflib/vcfcheck/.lint_skip b/tool_collections/vcflib/vcfcheck/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tool_collections/vcflib/vcfcheck/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tool_collections/vcflib/vcfgeno2haplo/.lint_skip b/tool_collections/vcflib/vcfgeno2haplo/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tool_collections/vcflib/vcfgeno2haplo/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tool_collections/vcflib/vcfleftalign/.lint_skip b/tool_collections/vcflib/vcfleftalign/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tool_collections/vcflib/vcfleftalign/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tool_collections/vcflib/vcfprimers/.lint_skip b/tool_collections/vcflib/vcfprimers/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tool_collections/vcflib/vcfprimers/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tool_collections/vcflib/vcfrandomsample/.lint_skip b/tool_collections/vcflib/vcfrandomsample/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tool_collections/vcflib/vcfrandomsample/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tool_collections/vcflib/vcfvcfintersect/.lint_skip b/tool_collections/vcflib/vcfvcfintersect/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tool_collections/vcflib/vcfvcfintersect/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/abricate/.lint_skip b/tools/abricate/.lint_skip index 2a25b72db67..d82e1c44e2d 100644 --- a/tools/abricate/.lint_skip +++ b/tools/abricate/.lint_skip @@ -1 +1,2 @@ InputsMissing +TestsCaseValidation diff --git a/tools/adapter_removal/.lint_skip b/tools/adapter_removal/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/adapter_removal/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/add_input_name_as_column/.lint_skip b/tools/add_input_name_as_column/.lint_skip index 46f5e08e85b..a5aef4c7624 100644 --- a/tools/add_input_name_as_column/.lint_skip +++ b/tools/add_input_name_as_column/.lint_skip @@ -1 +1,2 @@ CitationsMissing +TestsCaseValidation diff --git a/tools/aegean/.lint_skip b/tools/aegean/.lint_skip new file mode 100644 index 00000000000..f530e93cdd0 --- /dev/null +++ b/tools/aegean/.lint_skip @@ -0,0 +1,2 @@ +TestsCaseValidation +TestsParamInInputs diff --git a/tools/aldex2/.lint_skip b/tools/aldex2/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/aldex2/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/allegro/.lint_skip b/tools/allegro/.lint_skip index a68d017209e..1f78d73fa84 100644 --- a/tools/allegro/.lint_skip +++ b/tools/allegro/.lint_skip @@ -1 +1,2 @@ +TestsCaseValidation XMLOrder diff --git a/tools/amplican/.lint_skip b/tools/amplican/.lint_skip new file mode 100644 index 00000000000..f530e93cdd0 --- /dev/null +++ b/tools/amplican/.lint_skip @@ -0,0 +1,2 @@ +TestsCaseValidation +TestsParamInInputs diff --git a/tools/ampvis2/.lint_skip b/tools/ampvis2/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/ampvis2/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/amrfinderplus/.lint_skip b/tools/amrfinderplus/.lint_skip new file mode 100644 index 00000000000..329748981d8 --- /dev/null +++ b/tools/amrfinderplus/.lint_skip @@ -0,0 +1,6 @@ +OutputsFilterExpression): Filter ' input_option['input_mode']['input_select'] in ['nucleotide', 'nucl_prot'] and input_option['input_mode']['nucleotide_flank5_size'] != 0 ' is no valid expression: unexpected indent (, line 1 +OutputsFilterExpression): Filter ' input_option['input_mode']['input_select'] in ['nucleotide', 'nucl_prot'] ' is no valid expression: unexpected indent (, line 1 +OutputsFilterExpression): Filter ' input_option['input_mode']['input_select'] in ['protein', 'nucl_prot']' is no valid expression: unexpected indent (, line 1 +OutputsFilterExpression): Filter ' organism_options['organism_conditionnal']['organism_select'] == "add_organism" and organism_options['organism_conditionnal']['mutation_all'] is True ' is no valid expression: unexpected indent (, line 1 +TestsCaseValidation +TestsParamInInputs diff --git a/tools/anndata/.lint_skip b/tools/anndata/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/anndata/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/arriba/.lint_skip b/tools/arriba/.lint_skip new file mode 100644 index 00000000000..8ad0d1bc146 --- /dev/null +++ b/tools/arriba/.lint_skip @@ -0,0 +1,3 @@ +OutputsFilterExpression): Filter ' output_fusions_discarded == True' is no valid expression: unexpected indent (, line 1 +OutputsFilterExpression): Filter ' output_fusions_vcf == True' is no valid expression: unexpected indent (, line 1 +TestsCaseValidation diff --git a/tools/art/.lint_skip b/tools/art/.lint_skip index de67bcbc665..371a5f9499f 100644 --- a/tools/art/.lint_skip +++ b/tools/art/.lint_skip @@ -1,4 +1,5 @@ ConditionalParamTypeBool OutputsLabelDuplicatedFilter +TestsCaseValidation TestsExpectNumOutputs XMLOrder diff --git a/tools/artic/.lint_skip b/tools/artic/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/artic/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/augustus/.lint_skip b/tools/augustus/.lint_skip index e69de29bb2d..2092d1d0d68 100644 --- a/tools/augustus/.lint_skip +++ b/tools/augustus/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/b2btools/.lint_skip b/tools/b2btools/.lint_skip index e7d00398ee9..3f2477ee723 100644 --- a/tools/b2btools/.lint_skip +++ b/tools/b2btools/.lint_skip @@ -1 +1,2 @@ InputsNameRedundantArgument +TestsCaseValidation diff --git a/tools/bamutil/.lint_skip b/tools/bamutil/.lint_skip index 799954db976..19cdf057f54 100644 --- a/tools/bamutil/.lint_skip +++ b/tools/bamutil/.lint_skip @@ -1 +1 @@ -OutputsLabelDuplicatedFilter \ No newline at end of file +OutputsLabelDuplicatedFilterTestsCaseValidation diff --git a/tools/bandage/.lint_skip b/tools/bandage/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/bandage/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/barcode_splitter/.lint_skip b/tools/barcode_splitter/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/barcode_splitter/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/basil/.lint_skip b/tools/basil/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/basil/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/bayescan/.lint_skip b/tools/bayescan/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/bayescan/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/bbtools/.lint_skip b/tools/bbtools/.lint_skip new file mode 100644 index 00000000000..0f95134c0cd --- /dev/null +++ b/tools/bbtools/.lint_skip @@ -0,0 +1,2 @@ +OutputsFilterExpression): Filter 'None' is no valid expression: compile( +TestsCaseValidation diff --git a/tools/bcftools/.lint_skip b/tools/bcftools/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/bcftools/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/beacon2-import/.lint_skip b/tools/beacon2-import/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/beacon2-import/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/beagle/.lint_skip b/tools/beagle/.lint_skip index d710671f533..3c8f09ef4e9 100644 --- a/tools/beagle/.lint_skip +++ b/tools/beagle/.lint_skip @@ -1 +1,2 @@ +TestsParamInInputs ToolVersionPEP404 diff --git a/tools/bedtools/.lint_skip b/tools/bedtools/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/bedtools/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/bigscape/.lint_skip b/tools/bigscape/.lint_skip new file mode 100644 index 00000000000..e8a0661263f --- /dev/null +++ b/tools/bigscape/.lint_skip @@ -0,0 +1 @@ +OutputsFilterExpression): Filter ' clans_off == False ' is no valid expression: unexpected indent (, line 1 diff --git a/tools/bigwig_outlier_bed/.lint_skip b/tools/bigwig_outlier_bed/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/bigwig_outlier_bed/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/bioext/.lint_skip b/tools/bioext/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/bioext/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/bioinformatics_cafe/.lint_skip b/tools/bioinformatics_cafe/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/bioinformatics_cafe/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/biom_format/.lint_skip b/tools/biom_format/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/biom_format/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/blast/.lint_skip b/tools/blast/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/blast/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/bowtie2/.lint_skip b/tools/bowtie2/.lint_skip index 5e180cb3ab4..34f52fc1aad 100644 --- a/tools/bowtie2/.lint_skip +++ b/tools/bowtie2/.lint_skip @@ -1 +1,3 @@ ConditionalParamTypeBool +OutputsFilterExpression): Filter 'None' is no valid expression: compile( +TestsCaseValidation diff --git a/tools/bracken/.lint_skip b/tools/bracken/.lint_skip new file mode 100644 index 00000000000..12dc6476dec --- /dev/null +++ b/tools/bracken/.lint_skip @@ -0,0 +1 @@ +OutputsFilterExpression): Filter ' logfile_output == True ' is no valid expression: unexpected indent (, line 1 diff --git a/tools/breseq/.lint_skip b/tools/breseq/.lint_skip index d3e0aac05cd..37cbde00619 100644 --- a/tools/breseq/.lint_skip +++ b/tools/breseq/.lint_skip @@ -1,3 +1,4 @@ InputsNameRedundantArgument +TestsCaseValidation TestsExpectNumOutputs XMLOrder diff --git a/tools/bwa/.lint_skip b/tools/bwa/.lint_skip index 5e180cb3ab4..34f52fc1aad 100644 --- a/tools/bwa/.lint_skip +++ b/tools/bwa/.lint_skip @@ -1 +1,3 @@ ConditionalParamTypeBool +OutputsFilterExpression): Filter 'None' is no valid expression: compile( +TestsCaseValidation diff --git a/tools/bwa_mem2/.lint_skip b/tools/bwa_mem2/.lint_skip index 726b67ea618..2773a923f17 100644 --- a/tools/bwa_mem2/.lint_skip +++ b/tools/bwa_mem2/.lint_skip @@ -1,2 +1,4 @@ ConditionalParamTypeBool +OutputsFilterExpression): Filter 'None' is no valid expression: compile( +TestsCaseValidation XMLOrder diff --git a/tools/bwameth/.lint_skip b/tools/bwameth/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/bwameth/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/cdhit/.lint_skip b/tools/cdhit/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/cdhit/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/checkm/.lint_skip b/tools/checkm/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/checkm/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/chewbbaca/.lint_skip b/tools/chewbbaca/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/chewbbaca/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/chira/.lint_skip b/tools/chira/.lint_skip index f98c941cb66..9d4fa5be38f 100644 --- a/tools/chira/.lint_skip +++ b/tools/chira/.lint_skip @@ -1 +1,2 @@ CitationsNoValid +TestsCaseValidation diff --git a/tools/chromeister/.lint_skip b/tools/chromeister/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/chromeister/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/circos/.lint_skip b/tools/circos/.lint_skip index cc60dd28c7b..9a302b99483 100644 --- a/tools/circos/.lint_skip +++ b/tools/circos/.lint_skip @@ -1 +1,2 @@ +TestsCaseValidation TestsExpectNumOutputs diff --git a/tools/clustalw/.lint_skip b/tools/clustalw/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/clustalw/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/cnvkit/.lint_skip b/tools/cnvkit/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/cnvkit/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/codeml/.lint_skip b/tools/codeml/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/codeml/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/cojac/.lint_skip b/tools/cojac/.lint_skip new file mode 100644 index 00000000000..f530e93cdd0 --- /dev/null +++ b/tools/cojac/.lint_skip @@ -0,0 +1,2 @@ +TestsCaseValidation +TestsParamInInputs diff --git a/tools/colabfold/.lint_skip b/tools/colabfold/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/colabfold/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/collection_column_join/.lint_skip b/tools/collection_column_join/.lint_skip index 0d0dda5a1ff..3057ce9201a 100644 --- a/tools/collection_column_join/.lint_skip +++ b/tools/collection_column_join/.lint_skip @@ -1,3 +1,4 @@ CitationsNoValid OutputsLabelDuplicatedFilter +TestsCaseValidation TestsExpectNumOutputs diff --git a/tools/column_maker/.lint_skip b/tools/column_maker/.lint_skip index f98c941cb66..9d4fa5be38f 100644 --- a/tools/column_maker/.lint_skip +++ b/tools/column_maker/.lint_skip @@ -1 +1,2 @@ CitationsNoValid +TestsCaseValidation diff --git a/tools/column_remove_by_header/.lint_skip b/tools/column_remove_by_header/.lint_skip index f98c941cb66..9d4fa5be38f 100644 --- a/tools/column_remove_by_header/.lint_skip +++ b/tools/column_remove_by_header/.lint_skip @@ -1 +1,2 @@ CitationsNoValid +TestsCaseValidation diff --git a/tools/concoct/.lint_skip b/tools/concoct/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/concoct/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/cosg/.lint_skip b/tools/cosg/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/cosg/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/coverm/.lint_skip b/tools/coverm/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/coverm/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/crispr_studio/.lint_skip b/tools/crispr_studio/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/crispr_studio/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/crossmap/.lint_skip b/tools/crossmap/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/crossmap/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/cutadapt/.lint_skip b/tools/cutadapt/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/cutadapt/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/cwpair2/.lint_skip b/tools/cwpair2/.lint_skip index cc60dd28c7b..9a302b99483 100644 --- a/tools/cwpair2/.lint_skip +++ b/tools/cwpair2/.lint_skip @@ -1 +1,2 @@ +TestsCaseValidation TestsExpectNumOutputs diff --git a/tools/dada2/.lint_skip b/tools/dada2/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/dada2/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/deepmicro/.lint_skip b/tools/deepmicro/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/deepmicro/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/delly/.lint_skip b/tools/delly/.lint_skip new file mode 100644 index 00000000000..f530e93cdd0 --- /dev/null +++ b/tools/delly/.lint_skip @@ -0,0 +1,2 @@ +TestsCaseValidation +TestsParamInInputs diff --git a/tools/deseq2/.lint_skip b/tools/deseq2/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/deseq2/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/dexseq/.lint_skip b/tools/dexseq/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/dexseq/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/diamond/.lint_skip b/tools/diamond/.lint_skip index ef8b8e468d5..132d75042b4 100644 --- a/tools/diamond/.lint_skip +++ b/tools/diamond/.lint_skip @@ -1,2 +1,3 @@ InputsNameRedundantArgument OutputsLabelDuplicatedFilter +TestsCaseValidation diff --git a/tools/diffbind/.lint_skip b/tools/diffbind/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/diffbind/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/dimet/.lint_skip b/tools/dimet/.lint_skip new file mode 100644 index 00000000000..f530e93cdd0 --- /dev/null +++ b/tools/dimet/.lint_skip @@ -0,0 +1,2 @@ +TestsCaseValidation +TestsParamInInputs diff --git a/tools/disco/.lint_skip b/tools/disco/.lint_skip index 848f337dbe2..db1b8e87882 100644 --- a/tools/disco/.lint_skip +++ b/tools/disco/.lint_skip @@ -1,4 +1,5 @@ CitationsNoValid InputsNameDuplicateOutput +TestsCaseValidation TestsExpectNumOutputs XMLOrder diff --git a/tools/dram/.lint_skip b/tools/dram/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/dram/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/drep/.lint_skip b/tools/drep/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/drep/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/dropletutils/.lint_skip b/tools/dropletutils/.lint_skip new file mode 100644 index 00000000000..f530e93cdd0 --- /dev/null +++ b/tools/dropletutils/.lint_skip @@ -0,0 +1,2 @@ +TestsCaseValidation +TestsParamInInputs diff --git a/tools/edger/.lint_skip b/tools/edger/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/edger/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/egsea/.lint_skip b/tools/egsea/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/egsea/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/emboss_5/.lint_skip b/tools/emboss_5/.lint_skip index f743e01720f..c7e22043921 100644 --- a/tools/emboss_5/.lint_skip +++ b/tools/emboss_5/.lint_skip @@ -1,5 +1,6 @@ InputsSelectOptionDuplicateText OutputsLabelDuplicatedNoFilter +TestsCaseValidation TestsMissing TestsParamInInputs ToolIDWhitespace diff --git a/tools/ena_upload/.lint_skip b/tools/ena_upload/.lint_skip new file mode 100644 index 00000000000..34af741287c --- /dev/null +++ b/tools/ena_upload/.lint_skip @@ -0,0 +1,2 @@ +OutputsFilterExpression): Filter ' action_options['input_format_conditional']['input_format'] == "build_tables" or action_options['input_format_conditional']['input_format'] == "excel_tables" or action_options['input_format_conditional']['input_format'] == "isa_json"' is no valid expression: unexpected indent (, line 1 +TestsCaseValidation diff --git a/tools/ensembl_vep/.lint_skip b/tools/ensembl_vep/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/ensembl_vep/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/episcanpy/.lint_skip b/tools/episcanpy/.lint_skip new file mode 100644 index 00000000000..f530e93cdd0 --- /dev/null +++ b/tools/episcanpy/.lint_skip @@ -0,0 +1,2 @@ +TestsCaseValidation +TestsParamInInputs diff --git a/tools/evidencemodeler/.lint_skip b/tools/evidencemodeler/.lint_skip new file mode 100644 index 00000000000..f530e93cdd0 --- /dev/null +++ b/tools/evidencemodeler/.lint_skip @@ -0,0 +1,2 @@ +TestsCaseValidation +TestsParamInInputs diff --git a/tools/export2graphlan/.lint_skip b/tools/export2graphlan/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/export2graphlan/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/extract_genomic_dna/.lint_skip b/tools/extract_genomic_dna/.lint_skip index 709ca00eeae..86077aa1cb7 100644 --- a/tools/extract_genomic_dna/.lint_skip +++ b/tools/extract_genomic_dna/.lint_skip @@ -1 +1,2 @@ +TestsCaseValidation ToolIDWhitespace diff --git a/tools/falco/.lint_skip b/tools/falco/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/falco/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/fargene/.lint_skip b/tools/fargene/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/fargene/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/fasta_nucleotide_color_plot/.lint_skip b/tools/fasta_nucleotide_color_plot/.lint_skip index a68d017209e..1f78d73fa84 100644 --- a/tools/fasta_nucleotide_color_plot/.lint_skip +++ b/tools/fasta_nucleotide_color_plot/.lint_skip @@ -1 +1,2 @@ +TestsCaseValidation XMLOrder diff --git a/tools/fastk/.lint_skip b/tools/fastk/.lint_skip new file mode 100644 index 00000000000..cf802977257 --- /dev/null +++ b/tools/fastk/.lint_skip @@ -0,0 +1 @@ +OutputsFilterExpression): Filter ' sorted_table['sorted_table_option'] != 'no' ' is no valid expression: unexpected indent (, line 1 diff --git a/tools/fastp/.lint_skip b/tools/fastp/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/fastp/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/fastq_dl/.lint_skip b/tools/fastq_dl/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/fastq_dl/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/fastqc/.lint_skip b/tools/fastqc/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/fastqc/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/fasttree/.lint_skip b/tools/fasttree/.lint_skip index 48f8d2ba903..a596b5964bc 100644 --- a/tools/fasttree/.lint_skip +++ b/tools/fasttree/.lint_skip @@ -1,2 +1,3 @@ -# the bool is used in a filter and an if statement of the command block which works InputsBoolDistinctValues +TestsCaseValidation +# the bool is used in a filter and an if statement of the command block which works diff --git a/tools/featurecounts/.lint_skip b/tools/featurecounts/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/featurecounts/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/fermikit/.lint_skip b/tools/fermikit/.lint_skip index d710671f533..db84bbeb2fd 100644 --- a/tools/fermikit/.lint_skip +++ b/tools/fermikit/.lint_skip @@ -1 +1,2 @@ +TestsCaseValidation ToolVersionPEP404 diff --git a/tools/filtlong/.lint_skip b/tools/filtlong/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/filtlong/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/flair/.lint_skip b/tools/flair/.lint_skip index e7d00398ee9..3f2477ee723 100644 --- a/tools/flair/.lint_skip +++ b/tools/flair/.lint_skip @@ -1 +1,2 @@ InputsNameRedundantArgument +TestsCaseValidation diff --git a/tools/flash/.lint_skip b/tools/flash/.lint_skip index 3cb4b53ca3f..53896305155 100644 --- a/tools/flash/.lint_skip +++ b/tools/flash/.lint_skip @@ -1,4 +1,5 @@ InputsBoolDistinctValues InputsNameRedundantArgument OutputsLabelDuplicatedFilter +TestsCaseValidation XMLOrder diff --git a/tools/freebayes/.lint_skip b/tools/freebayes/.lint_skip index d3e0aac05cd..37cbde00619 100644 --- a/tools/freebayes/.lint_skip +++ b/tools/freebayes/.lint_skip @@ -1,3 +1,4 @@ InputsNameRedundantArgument +TestsCaseValidation TestsExpectNumOutputs XMLOrder diff --git a/tools/freec/.lint_skip b/tools/freec/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/freec/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/freyja/.lint_skip b/tools/freyja/.lint_skip new file mode 100644 index 00000000000..4835fb975a3 --- /dev/null +++ b/tools/freyja/.lint_skip @@ -0,0 +1,2 @@ +OutputsFilterExpression +TestsCaseValidation diff --git a/tools/funannotate/.lint_skip b/tools/funannotate/.lint_skip new file mode 100644 index 00000000000..93b5ffc68a8 --- /dev/null +++ b/tools/funannotate/.lint_skip @@ -0,0 +1 @@ +BioToolsValid diff --git a/tools/gatk4/.lint_skip b/tools/gatk4/.lint_skip index 6eb36d713a8..e8dce65f78e 100644 --- a/tools/gatk4/.lint_skip +++ b/tools/gatk4/.lint_skip @@ -1,5 +1,6 @@ InputsNameDuplicate InputsNameRedundantArgument +TestsCaseValidation TestsExpectNumOutputs TestsParamInInputs ToolVersionPEP404 diff --git a/tools/gecko/.lint_skip b/tools/gecko/.lint_skip new file mode 100644 index 00000000000..7f2fd43ebfc --- /dev/null +++ b/tools/gecko/.lint_skip @@ -0,0 +1 @@ +OutputsFilterExpression): Filter ' selection_mode == 'alignments'' is no valid expression: unexpected indent (, line 1 diff --git a/tools/gemini/.lint_skip b/tools/gemini/.lint_skip index 5bade0f665b..0ed47b5b2d2 100644 --- a/tools/gemini/.lint_skip +++ b/tools/gemini/.lint_skip @@ -2,4 +2,6 @@ InputsDataOptionsFilterAttribFiltersType InputsDataOptionsFiltersRef InputsDataOptionsFiltersType InputsNameRedundantArgument +TestsCaseValidation +TestsParamInInputs XMLOrder diff --git a/tools/genebed_maf_to_fasta/.lint_skip b/tools/genebed_maf_to_fasta/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/genebed_maf_to_fasta/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/genehunter_modscore/.lint_skip b/tools/genehunter_modscore/.lint_skip index 5e180cb3ab4..98e4c384ead 100644 --- a/tools/genehunter_modscore/.lint_skip +++ b/tools/genehunter_modscore/.lint_skip @@ -1 +1,2 @@ ConditionalParamTypeBool +TestsCaseValidation diff --git a/tools/geneiobio/.lint_skip b/tools/geneiobio/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/geneiobio/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/genetrack/.lint_skip b/tools/genetrack/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/genetrack/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/genomic_super_signature/.lint_skip b/tools/genomic_super_signature/.lint_skip index a68d017209e..1f78d73fa84 100644 --- a/tools/genomic_super_signature/.lint_skip +++ b/tools/genomic_super_signature/.lint_skip @@ -1 +1,2 @@ +TestsCaseValidation XMLOrder diff --git a/tools/genrich/.lint_skip b/tools/genrich/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/genrich/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/getorganelle/.lint_skip b/tools/getorganelle/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/getorganelle/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/gffcompare/.lint_skip b/tools/gffcompare/.lint_skip index c9dfa9bcef8..3ff3d024bef 100644 --- a/tools/gffcompare/.lint_skip +++ b/tools/gffcompare/.lint_skip @@ -1,2 +1,4 @@ # outputs have disjoint filters OutputsLabelDuplicatedFilter +TestsCaseValidation): Serious problem parsing tool source or tests - cannot validate test cases. The exception is [Invalid conditional test value (Yes) for parameter (selector +TestsParamInInputs diff --git a/tools/gffread/.lint_skip b/tools/gffread/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/gffread/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/ggplot2/.lint_skip b/tools/ggplot2/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/ggplot2/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/glimmer/.lint_skip b/tools/glimmer/.lint_skip index 522ad865ff6..6a2ed9303f7 100644 --- a/tools/glimmer/.lint_skip +++ b/tools/glimmer/.lint_skip @@ -1,5 +1,6 @@ CommandTODO InputsBoolDistinctValues OutputsLabelDuplicatedNoFilter +TestsCaseValidation TestsExpectNumOutputs XMLOrder diff --git a/tools/goseq/.lint_skip b/tools/goseq/.lint_skip index a68d017209e..1f78d73fa84 100644 --- a/tools/goseq/.lint_skip +++ b/tools/goseq/.lint_skip @@ -1 +1,2 @@ +TestsCaseValidation XMLOrder diff --git a/tools/gprofiler/.lint_skip b/tools/gprofiler/.lint_skip index cc60dd28c7b..9a302b99483 100644 --- a/tools/gprofiler/.lint_skip +++ b/tools/gprofiler/.lint_skip @@ -1 +1,2 @@ +TestsCaseValidation TestsExpectNumOutputs diff --git a/tools/graphembed/.lint_skip b/tools/graphembed/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/graphembed/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/graphlan/.lint_skip b/tools/graphlan/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/graphlan/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/groot/.lint_skip b/tools/groot/.lint_skip new file mode 100644 index 00000000000..f530e93cdd0 --- /dev/null +++ b/tools/groot/.lint_skip @@ -0,0 +1,2 @@ +TestsCaseValidation +TestsParamInInputs diff --git a/tools/gtfToBed12/.lint_skip b/tools/gtfToBed12/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/gtfToBed12/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/gubbins/.lint_skip b/tools/gubbins/.lint_skip new file mode 100644 index 00000000000..f530e93cdd0 --- /dev/null +++ b/tools/gubbins/.lint_skip @@ -0,0 +1,2 @@ +TestsCaseValidation +TestsParamInInputs diff --git a/tools/gvcftools/.lint_skip b/tools/gvcftools/.lint_skip index e7d00398ee9..3f2477ee723 100644 --- a/tools/gvcftools/.lint_skip +++ b/tools/gvcftools/.lint_skip @@ -1 +1,2 @@ InputsNameRedundantArgument +TestsCaseValidation diff --git a/tools/gwastools/.lint_skip b/tools/gwastools/.lint_skip new file mode 100644 index 00000000000..70d8f55ae3b --- /dev/null +++ b/tools/gwastools/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation): Serious problem parsing tool source or tests - cannot validate test cases. The exception is [Invalid conditional test value (yes) for parameter (thinning diff --git a/tools/hansel/.lint_skip b/tools/hansel/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/hansel/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/hapcut2/.lint_skip b/tools/hapcut2/.lint_skip new file mode 100644 index 00000000000..f530e93cdd0 --- /dev/null +++ b/tools/hapcut2/.lint_skip @@ -0,0 +1,2 @@ +TestsCaseValidation +TestsParamInInputs diff --git a/tools/happy/.lint_skip b/tools/happy/.lint_skip index 46f5e08e85b..a5aef4c7624 100644 --- a/tools/happy/.lint_skip +++ b/tools/happy/.lint_skip @@ -1 +1,2 @@ CitationsMissing +TestsCaseValidation diff --git a/tools/heatmap2/.lint_skip b/tools/heatmap2/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/heatmap2/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/heinz/.lint_skip b/tools/heinz/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/heinz/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/hicexplorer/.lint_skip b/tools/hicexplorer/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/hicexplorer/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/hifiasm/.lint_skip b/tools/hifiasm/.lint_skip new file mode 100644 index 00000000000..f530e93cdd0 --- /dev/null +++ b/tools/hifiasm/.lint_skip @@ -0,0 +1,2 @@ +TestsCaseValidation +TestsParamInInputs diff --git a/tools/hifiasm_meta/.lint_skip b/tools/hifiasm_meta/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/hifiasm_meta/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/hisat2/.lint_skip b/tools/hisat2/.lint_skip index c4d48dac9f2..105e8650023 100644 --- a/tools/hisat2/.lint_skip +++ b/tools/hisat2/.lint_skip @@ -1,2 +1,4 @@ InputsNameRedundantArgument +OutputsFilterExpression): Filter 'None' is no valid expression: compile( +TestsCaseValidation TestsExpectNumOutputs diff --git a/tools/hmmer3/.lint_skip b/tools/hmmer3/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/hmmer3/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/homer/.lint_skip b/tools/homer/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/homer/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/htseq_count/.lint_skip b/tools/htseq_count/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/htseq_count/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/humann/.lint_skip b/tools/humann/.lint_skip new file mode 100644 index 00000000000..f530e93cdd0 --- /dev/null +++ b/tools/humann/.lint_skip @@ -0,0 +1,2 @@ +TestsCaseValidation +TestsParamInInputs diff --git a/tools/hybpiper/.lint_skip b/tools/hybpiper/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/hybpiper/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/hyphy/.lint_skip b/tools/hyphy/.lint_skip index cc60dd28c7b..9a302b99483 100644 --- a/tools/hyphy/.lint_skip +++ b/tools/hyphy/.lint_skip @@ -1 +1,2 @@ +TestsCaseValidation TestsExpectNumOutputs diff --git a/tools/hypo/.lint_skip b/tools/hypo/.lint_skip index a68d017209e..1f78d73fa84 100644 --- a/tools/hypo/.lint_skip +++ b/tools/hypo/.lint_skip @@ -1 +1,2 @@ +TestsCaseValidation XMLOrder diff --git a/tools/icescreen/.lint_skip b/tools/icescreen/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/icescreen/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/idr_download/.lint_skip b/tools/idr_download/.lint_skip index cc60dd28c7b..9a302b99483 100644 --- a/tools/idr_download/.lint_skip +++ b/tools/idr_download/.lint_skip @@ -1 +1,2 @@ +TestsCaseValidation TestsExpectNumOutputs diff --git a/tools/infercnv/.lint_skip b/tools/infercnv/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/infercnv/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/integron_finder/.lint_skip b/tools/integron_finder/.lint_skip new file mode 100644 index 00000000000..115832761d7 --- /dev/null +++ b/tools/integron_finder/.lint_skip @@ -0,0 +1,2 @@ +OutputsFilterExpression): Filter ' no_logfile == False' is no valid expression: unexpected indent (, line 1 +TestsCaseValidation diff --git a/tools/interval2maf/.lint_skip b/tools/interval2maf/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/interval2maf/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/intervene/.lint_skip b/tools/intervene/.lint_skip index a68d017209e..1f78d73fa84 100644 --- a/tools/intervene/.lint_skip +++ b/tools/intervene/.lint_skip @@ -1 +1,2 @@ +TestsCaseValidation XMLOrder diff --git a/tools/iqtree/.lint_skip b/tools/iqtree/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/iqtree/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/isescan/.lint_skip b/tools/isescan/.lint_skip new file mode 100644 index 00000000000..9f534312d15 --- /dev/null +++ b/tools/isescan/.lint_skip @@ -0,0 +1 @@ +OutputsFilterExpression): Filter ' log_activate == True ' is no valid expression: unexpected indent (, line 1 diff --git a/tools/isoformswitchanalyzer/.lint_skip b/tools/isoformswitchanalyzer/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/isoformswitchanalyzer/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/ivar/.lint_skip b/tools/ivar/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/ivar/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/iwtomics/.lint_skip b/tools/iwtomics/.lint_skip index a68d017209e..1f78d73fa84 100644 --- a/tools/iwtomics/.lint_skip +++ b/tools/iwtomics/.lint_skip @@ -1 +1,2 @@ +TestsCaseValidation XMLOrder diff --git a/tools/jbrowse/.lint_skip b/tools/jbrowse/.lint_skip index 619947ad80b..c2747c3a028 100644 --- a/tools/jbrowse/.lint_skip +++ b/tools/jbrowse/.lint_skip @@ -1,3 +1,4 @@ ConditionalParamTypeBool +TestsCaseValidation TestsMissing XMLOrder diff --git a/tools/jellyfish/.lint_skip b/tools/jellyfish/.lint_skip index e7d00398ee9..d59959c1f96 100644 --- a/tools/jellyfish/.lint_skip +++ b/tools/jellyfish/.lint_skip @@ -1 +1,3 @@ InputsNameRedundantArgument +TestsCaseValidation +TestsParamInInputs diff --git a/tools/jq/.lint_skip b/tools/jq/.lint_skip index f98c941cb66..9d4fa5be38f 100644 --- a/tools/jq/.lint_skip +++ b/tools/jq/.lint_skip @@ -1 +1,2 @@ CitationsNoValid +TestsCaseValidation diff --git a/tools/kallisto/.lint_skip b/tools/kallisto/.lint_skip index cc60dd28c7b..9a302b99483 100644 --- a/tools/kallisto/.lint_skip +++ b/tools/kallisto/.lint_skip @@ -1 +1,2 @@ +TestsCaseValidation TestsExpectNumOutputs diff --git a/tools/kc-align/.lint_skip b/tools/kc-align/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/kc-align/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/khmer/.lint_skip b/tools/khmer/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/khmer/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/kleborate/.lint_skip b/tools/kleborate/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/kleborate/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/kma/.lint_skip b/tools/kma/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/kma/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/kofamscan/.lint_skip b/tools/kofamscan/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/kofamscan/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/krakentools/.lint_skip b/tools/krakentools/.lint_skip new file mode 100644 index 00000000000..4835fb975a3 --- /dev/null +++ b/tools/krakentools/.lint_skip @@ -0,0 +1,2 @@ +OutputsFilterExpression +TestsCaseValidation diff --git a/tools/krocus/.lint_skip b/tools/krocus/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/krocus/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/last/.lint_skip b/tools/last/.lint_skip new file mode 100644 index 00000000000..f530e93cdd0 --- /dev/null +++ b/tools/last/.lint_skip @@ -0,0 +1,2 @@ +TestsCaseValidation +TestsParamInInputs diff --git a/tools/lastz/.lint_skip b/tools/lastz/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/lastz/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/length_and_gc_content/.lint_skip b/tools/length_and_gc_content/.lint_skip index f98c941cb66..9d4fa5be38f 100644 --- a/tools/length_and_gc_content/.lint_skip +++ b/tools/length_and_gc_content/.lint_skip @@ -1 +1,2 @@ CitationsNoValid +TestsCaseValidation diff --git a/tools/limma_voom/.lint_skip b/tools/limma_voom/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/limma_voom/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/links/.lint_skip b/tools/links/.lint_skip index aaf98e466e4..44409480c2c 100644 --- a/tools/links/.lint_skip +++ b/tools/links/.lint_skip @@ -1,2 +1,3 @@ +TestsCaseValidation ToolVersionPEP404 XMLOrder diff --git a/tools/lofreq/.lint_skip b/tools/lofreq/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/lofreq/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/lorikeet/.lint_skip b/tools/lorikeet/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/lorikeet/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/macs2/.lint_skip b/tools/macs2/.lint_skip new file mode 100644 index 00000000000..aa732772c5b --- /dev/null +++ b/tools/macs2/.lint_skip @@ -0,0 +1,4 @@ +OutputsFilterExpression +OutputsFilterExpression): Filter ' outputs and 'peaks_tabular' in outputs' is no valid expression: unexpected indent (, line 1 +TestsCaseValidation +TestsCaseValidation): Serious problem parsing tool source or tests - cannot validate test cases. The exception is [invalid literal for int( diff --git a/tools/maf_stats/.lint_skip b/tools/maf_stats/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/maf_stats/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/mageck/.lint_skip b/tools/mageck/.lint_skip index d3e0aac05cd..37cbde00619 100644 --- a/tools/mageck/.lint_skip +++ b/tools/mageck/.lint_skip @@ -1,3 +1,4 @@ InputsNameRedundantArgument +TestsCaseValidation TestsExpectNumOutputs XMLOrder diff --git a/tools/maker/.lint_skip b/tools/maker/.lint_skip index 9b777a1b5b6..ac06880c07b 100644 --- a/tools/maker/.lint_skip +++ b/tools/maker/.lint_skip @@ -1,2 +1,3 @@ InputsNameRedundantArgument +TestsCaseValidation XMLOrder diff --git a/tools/malt/.lint_skip b/tools/malt/.lint_skip index 5e180cb3ab4..98e4c384ead 100644 --- a/tools/malt/.lint_skip +++ b/tools/malt/.lint_skip @@ -1 +1,2 @@ ConditionalParamTypeBool +TestsCaseValidation diff --git a/tools/mapseq/.lint_skip b/tools/mapseq/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/mapseq/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/mash/.lint_skip b/tools/mash/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/mash/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/masigpro/.lint_skip b/tools/masigpro/.lint_skip index eb2cdb1921c..ec86378b754 100644 --- a/tools/masigpro/.lint_skip +++ b/tools/masigpro/.lint_skip @@ -1,2 +1,4 @@ ConditionalParamTypeBool +OutputsFilterExpression +TestsCaseValidation TestsExpectNumOutputs diff --git a/tools/maxbin2/.lint_skip b/tools/maxbin2/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/maxbin2/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/mcl/.lint_skip b/tools/mcl/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/mcl/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/megan/.lint_skip b/tools/megan/.lint_skip index 17796d16c43..40dc10d7985 100644 --- a/tools/megan/.lint_skip +++ b/tools/megan/.lint_skip @@ -1,2 +1,3 @@ ConditionalParamTypeBool InputsNameRedundantArgument +TestsCaseValidation diff --git a/tools/meme/.lint_skip b/tools/meme/.lint_skip index d3e0aac05cd..a8d442eb3e8 100644 --- a/tools/meme/.lint_skip +++ b/tools/meme/.lint_skip @@ -1,3 +1,5 @@ InputsNameRedundantArgument +OutputsFilterExpression): Filter 'None' is no valid expression: compile( +TestsCaseValidation TestsExpectNumOutputs XMLOrder diff --git a/tools/meme_chip/.lint_skip b/tools/meme_chip/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/meme_chip/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/merlin/.lint_skip b/tools/merlin/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/merlin/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/meryl/.lint_skip b/tools/meryl/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/meryl/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/metabat2/.lint_skip b/tools/metabat2/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/metabat2/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/metabuli/.lint_skip b/tools/metabuli/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/metabuli/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/metaeuk/.lint_skip b/tools/metaeuk/.lint_skip index 375df7b32b6..7965d0423cc 100644 --- a/tools/metaeuk/.lint_skip +++ b/tools/metaeuk/.lint_skip @@ -1,2 +1,2 @@ +ToolVersionPEP404 # we can't change that -ToolVersionPEP404 \ No newline at end of file diff --git a/tools/metaphlan/.lint_skip b/tools/metaphlan/.lint_skip new file mode 100644 index 00000000000..f530e93cdd0 --- /dev/null +++ b/tools/metaphlan/.lint_skip @@ -0,0 +1,2 @@ +TestsCaseValidation +TestsParamInInputs diff --git a/tools/metawrapmg/.lint_skip b/tools/metawrapmg/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/metawrapmg/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/mg_toolkit/.lint_skip b/tools/mg_toolkit/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/mg_toolkit/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/migmap/.lint_skip b/tools/migmap/.lint_skip index a68d017209e..1f78d73fa84 100644 --- a/tools/migmap/.lint_skip +++ b/tools/migmap/.lint_skip @@ -1 +1,2 @@ +TestsCaseValidation XMLOrder diff --git a/tools/miniasm/.lint_skip b/tools/miniasm/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/miniasm/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/minimap2/.lint_skip b/tools/minimap2/.lint_skip new file mode 100644 index 00000000000..0f95134c0cd --- /dev/null +++ b/tools/minimap2/.lint_skip @@ -0,0 +1,2 @@ +OutputsFilterExpression): Filter 'None' is no valid expression: compile( +TestsCaseValidation diff --git a/tools/miniprot/.lint_skip b/tools/miniprot/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/miniprot/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/mirnature/.lint_skip b/tools/mirnature/.lint_skip index 561ac4b4543..68fda2339e5 100644 --- a/tools/mirnature/.lint_skip +++ b/tools/mirnature/.lint_skip @@ -1,2 +1,5 @@ +OutputsFilterExpression): Filter ' stage == "complete" ' is no valid expression: unexpected indent (, line 1 +OutputsFilterExpression): Filter ' stage == "homology" ' is no valid expression: unexpected indent (, line 1 OutputsLabelDuplicatedFilter +TestsCaseValidation TestsExpectNumOutputs diff --git a/tools/mlst/.lint_skip b/tools/mlst/.lint_skip index ee3065a51c9..40ae0aea8c7 100644 --- a/tools/mlst/.lint_skip +++ b/tools/mlst/.lint_skip @@ -1,2 +1,3 @@ +TestsCaseValidation TestsExpectNumOutputs XMLOrder diff --git a/tools/moabs/.lint_skip b/tools/moabs/.lint_skip new file mode 100644 index 00000000000..d5a9e76c444 --- /dev/null +++ b/tools/moabs/.lint_skip @@ -0,0 +1,6 @@ +OutputsFilterExpression): Filter ' "1" in output_selector ' is no valid expression: unexpected indent (, line 1 +OutputsFilterExpression): Filter ' "2" in output_selector ' is no valid expression: unexpected indent (, line 1 +OutputsFilterExpression): Filter ' "3" in output_selector ' is no valid expression: unexpected indent (, line 1 +OutputsFilterExpression): Filter ' "4" in output_selector ' is no valid expression: unexpected indent (, line 1 +OutputsFilterExpression): Filter ' "5" in output_selector ' is no valid expression: unexpected indent (, line 1 +TestsCaseValidation diff --git a/tools/mothur/.lint_skip b/tools/mothur/.lint_skip index c538ac8fe2f..0e3b5235c40 100644 --- a/tools/mothur/.lint_skip +++ b/tools/mothur/.lint_skip @@ -1,5 +1,15 @@ HelpInvalidRST +OutputsFilterExpression): Filter ' $constaxonomy ' is no valid expression: unexpected indent (, line 1 +OutputsFilterExpression): Filter ' $corraxes ' is no valid expression: unexpected indent (, line 1 +OutputsFilterExpression): Filter ' $list ' is no valid expression: unexpected indent (, line 1 +OutputsFilterExpression): Filter ' $otucorr ' is no valid expression: unexpected indent (, line 1 +OutputsFilterExpression): Filter ' $shared ' is no valid expression: unexpected indent (, line 1 +OutputsFilterExpression): Filter ' format == "count" ' is no valid expression: unexpected indent (, line 1 +OutputsFilterExpression): Filter ' format == "name" ' is no valid expression: unexpected indent (, line 1 +OutputsFilterExpression): Filter ' m['method'] == 'dmm' ' is no valid expression: unexpected indent (, line 1 +OutputsFilterExpression): Filter 'search['type'] == 'list' or (search['type'] == 'name' and split['dosplit'] == 'yes'' is no valid expression: '(' was never closed (, line 1 OutputsLabelDuplicatedFilter OutputsNameInvalidCheetah +TestsCaseValidation TestsExpectNumOutputs TestsParamInInputs diff --git a/tools/multigps/.lint_skip b/tools/multigps/.lint_skip index cc60dd28c7b..9a302b99483 100644 --- a/tools/multigps/.lint_skip +++ b/tools/multigps/.lint_skip @@ -1 +1,2 @@ +TestsCaseValidation TestsExpectNumOutputs diff --git a/tools/multigsea/.lint_skip b/tools/multigsea/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/multigsea/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/multiqc/.lint_skip b/tools/multiqc/.lint_skip new file mode 100644 index 00000000000..f530e93cdd0 --- /dev/null +++ b/tools/multiqc/.lint_skip @@ -0,0 +1,2 @@ +TestsCaseValidation +TestsParamInInputs diff --git a/tools/mummer4/.lint_skip b/tools/mummer4/.lint_skip new file mode 100644 index 00000000000..537c3c0b382 --- /dev/null +++ b/tools/mummer4/.lint_skip @@ -0,0 +1,4 @@ +OutputsFilterExpression): Filter ' extra_outs == 'all' ' is no valid expression: unexpected indent (, line 1 +OutputsFilterExpression): Filter ' report_only == 'no' ' is no valid expression: unexpected indent (, line 1 +OutputsFilterExpression): Filter ' report_only == 'no'' is no valid expression: unexpected indent (, line 1 +TestsCaseValidation diff --git a/tools/mykrobe/.lint_skip b/tools/mykrobe/.lint_skip index a68d017209e..1f78d73fa84 100644 --- a/tools/mykrobe/.lint_skip +++ b/tools/mykrobe/.lint_skip @@ -1 +1,2 @@ +TestsCaseValidation XMLOrder diff --git a/tools/nanoplot/.lint_skip b/tools/nanoplot/.lint_skip new file mode 100644 index 00000000000..f530e93cdd0 --- /dev/null +++ b/tools/nanoplot/.lint_skip @@ -0,0 +1,2 @@ +TestsCaseValidation +TestsParamInInputs diff --git a/tools/ncbi_datasets/.lint_skip b/tools/ncbi_datasets/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/ncbi_datasets/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/ncbi_entrez_eutils/.lint_skip b/tools/ncbi_entrez_eutils/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/ncbi_entrez_eutils/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/ncbi_fcs_gx/.lint_skip b/tools/ncbi_fcs_gx/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/ncbi_fcs_gx/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/newick_utils/.lint_skip b/tools/newick_utils/.lint_skip index a68d017209e..1f78d73fa84 100644 --- a/tools/newick_utils/.lint_skip +++ b/tools/newick_utils/.lint_skip @@ -1 +1,2 @@ +TestsCaseValidation XMLOrder diff --git a/tools/nonpareil/.lint_skip b/tools/nonpareil/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/nonpareil/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/novoplasty/.lint_skip b/tools/novoplasty/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/novoplasty/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/obitools/.lint_skip b/tools/obitools/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/obitools/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/orthofinder/.lint_skip b/tools/orthofinder/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/orthofinder/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/pangolin/.lint_skip b/tools/pangolin/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/pangolin/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/pathview/.lint_skip b/tools/pathview/.lint_skip index ee3065a51c9..40ae0aea8c7 100644 --- a/tools/pathview/.lint_skip +++ b/tools/pathview/.lint_skip @@ -1,2 +1,3 @@ +TestsCaseValidation TestsExpectNumOutputs XMLOrder diff --git a/tools/pbgcpp/.lint_skip b/tools/pbgcpp/.lint_skip index 9c757f1de60..18d83886cf5 100644 --- a/tools/pbgcpp/.lint_skip +++ b/tools/pbgcpp/.lint_skip @@ -1,2 +1,3 @@ CitationsMissing +TestsCaseValidation TestsExpectNumOutputs diff --git a/tools/pbmm2/.lint_skip b/tools/pbmm2/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/pbmm2/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/pbtk/.lint_skip b/tools/pbtk/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/pbtk/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/peakzilla/.lint_skip b/tools/peakzilla/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/peakzilla/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/phyml/.lint_skip b/tools/phyml/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/phyml/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/picard/.lint_skip b/tools/picard/.lint_skip index 5e180cb3ab4..98e4c384ead 100644 --- a/tools/picard/.lint_skip +++ b/tools/picard/.lint_skip @@ -1 +1,2 @@ ConditionalParamTypeBool +TestsCaseValidation diff --git a/tools/picrust/.lint_skip b/tools/picrust/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/picrust/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/picrust2/.lint_skip b/tools/picrust2/.lint_skip index 208f465e2bc..d4ebd4bd211 100644 --- a/tools/picrust2/.lint_skip +++ b/tools/picrust2/.lint_skip @@ -1 +1,2 @@ +TestsCaseValidation TestsExpectNumOutputsFailing diff --git a/tools/pilon/.lint_skip b/tools/pilon/.lint_skip index eb2cdb1921c..62b87ca483d 100644 --- a/tools/pilon/.lint_skip +++ b/tools/pilon/.lint_skip @@ -1,2 +1,3 @@ ConditionalParamTypeBool +TestsCaseValidation TestsExpectNumOutputs diff --git a/tools/pizzly/.lint_skip b/tools/pizzly/.lint_skip index e7d00398ee9..3f2477ee723 100644 --- a/tools/pizzly/.lint_skip +++ b/tools/pizzly/.lint_skip @@ -1 +1,2 @@ InputsNameRedundantArgument +TestsCaseValidation diff --git a/tools/plasmidfinder/.lint_skip b/tools/plasmidfinder/.lint_skip new file mode 100644 index 00000000000..0a788394ded --- /dev/null +++ b/tools/plasmidfinder/.lint_skip @@ -0,0 +1,8 @@ +OutputsFilterExpression): Filter ' "data_json" in output_files['output_selection'] ' is no valid expression: unexpected indent (, line 1 +OutputsFilterExpression): Filter ' "hit_fasta" in output_files['output_selection'] ' is no valid expression: unexpected indent (, line 1 +OutputsFilterExpression): Filter ' "logfile" in output_files['output_selection'] ' is no valid expression: unexpected indent (, line 1 +OutputsFilterExpression): Filter ' "plasmid_fasta" in output_files['output_selection'] ' is no valid expression: unexpected indent (, line 1 +OutputsFilterExpression): Filter ' "result_tsv" in output_files['output_selection'] ' is no valid expression: unexpected indent (, line 1 +OutputsFilterExpression): Filter ' "result_txt" in output_files['output_selection'] ' is no valid expression: unexpected indent (, line 1 +TestsCaseValidation +TestsParamInInputs diff --git a/tools/plink/.lint_skip b/tools/plink/.lint_skip index d710671f533..db84bbeb2fd 100644 --- a/tools/plink/.lint_skip +++ b/tools/plink/.lint_skip @@ -1 +1,2 @@ +TestsCaseValidation ToolVersionPEP404 diff --git a/tools/polypolish/.lint_skip b/tools/polypolish/.lint_skip new file mode 100644 index 00000000000..879c128875a --- /dev/null +++ b/tools/polypolish/.lint_skip @@ -0,0 +1,3 @@ +OutputsFilterExpression): Filter ' options['debug'] == True ' is no valid expression: unexpected indent (, line 1 +OutputsFilterExpression): Filter ' options['keep_logfile'] == True ' is no valid expression: unexpected indent (, line 1 +TestsCaseValidation diff --git a/tools/porechop/.lint_skip b/tools/porechop/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/porechop/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/presto/.lint_skip b/tools/presto/.lint_skip index e69de29bb2d..2092d1d0d68 100644 --- a/tools/presto/.lint_skip +++ b/tools/presto/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/pretext/.lint_skip b/tools/pretext/.lint_skip new file mode 100644 index 00000000000..f530e93cdd0 --- /dev/null +++ b/tools/pretext/.lint_skip @@ -0,0 +1,2 @@ +TestsCaseValidation +TestsParamInInputs diff --git a/tools/prinseq/.lint_skip b/tools/prinseq/.lint_skip index 5c3b72bd205..f9186933fc6 100644 --- a/tools/prinseq/.lint_skip +++ b/tools/prinseq/.lint_skip @@ -1,2 +1,3 @@ OutputsLabelDuplicatedFilter +TestsCaseValidation XMLOrder diff --git a/tools/prot-scriber/.lint_skip b/tools/prot-scriber/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/prot-scriber/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/proteinortho/.lint_skip b/tools/proteinortho/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/proteinortho/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/pureclip/.lint_skip b/tools/pureclip/.lint_skip index cc60dd28c7b..9a302b99483 100644 --- a/tools/pureclip/.lint_skip +++ b/tools/pureclip/.lint_skip @@ -1 +1,2 @@ +TestsCaseValidation TestsExpectNumOutputs diff --git a/tools/purge_dups/.lint_skip b/tools/purge_dups/.lint_skip new file mode 100644 index 00000000000..f530e93cdd0 --- /dev/null +++ b/tools/purge_dups/.lint_skip @@ -0,0 +1,2 @@ +TestsCaseValidation +TestsParamInInputs diff --git a/tools/pyega3/.lint_skip b/tools/pyega3/.lint_skip new file mode 100644 index 00000000000..b88b0bb3f01 --- /dev/null +++ b/tools/pyega3/.lint_skip @@ -0,0 +1,6 @@ +OutputsFilterExpression): Filter ' action['action_type'] == 'download_file' ' is no valid expression: unexpected indent (, line 1 +OutputsFilterExpression): Filter ' action['action_type'] == 'download_files' ' is no valid expression: unexpected indent (, line 1 +OutputsFilterExpression): Filter ' action['action_type'] == 'list_dataset_files' ' is no valid expression: unexpected indent (, line 1 +OutputsFilterExpression): Filter ' action['action_type'] == 'list_datasets' ' is no valid expression: unexpected indent (, line 1 +OutputsFilterExpression): Filter ' output_log ' is no valid expression: unexpected indent (, line 1 +TestsCaseValidation diff --git a/tools/pygenometracks/.lint_skip b/tools/pygenometracks/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/pygenometracks/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/pysradb/.lint_skip b/tools/pysradb/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/pysradb/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/qfilt/.lint_skip b/tools/qfilt/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/qfilt/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/quast/.lint_skip b/tools/quast/.lint_skip new file mode 100644 index 00000000000..dd74cbaa6a0 --- /dev/null +++ b/tools/quast/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation): Serious problem parsing tool source or tests - cannot validate test cases. The exception is [Invalid conditional test value (--gene_finding) for parameter (tool diff --git a/tools/query_impc/.lint_skip b/tools/query_impc/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/query_impc/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/query_tabular/.lint_skip b/tools/query_tabular/.lint_skip new file mode 100644 index 00000000000..f530e93cdd0 --- /dev/null +++ b/tools/query_tabular/.lint_skip @@ -0,0 +1,2 @@ +TestsCaseValidation +TestsParamInInputs diff --git a/tools/quickmerge/.lint_skip b/tools/quickmerge/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/quickmerge/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/raceid/.lint_skip b/tools/raceid/.lint_skip index cc60dd28c7b..ccee25d9311 100644 --- a/tools/raceid/.lint_skip +++ b/tools/raceid/.lint_skip @@ -1 +1,3 @@ +TestsCaseValidation TestsExpectNumOutputs +TestsParamInInputs diff --git a/tools/rasusa/.lint_skip b/tools/rasusa/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/rasusa/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/raxml/.lint_skip b/tools/raxml/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/raxml/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/read_it_and_keep/.lint_skip b/tools/read_it_and_keep/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/read_it_and_keep/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/recentrifuge/.lint_skip b/tools/recentrifuge/.lint_skip new file mode 100644 index 00000000000..b43b8556e1b --- /dev/null +++ b/tools/recentrifuge/.lint_skip @@ -0,0 +1,7 @@ +OutputsFilterExpression): Filter ' output_option['extra'] == 'CSV' ' is no valid expression: unexpected indent (, line 1 +OutputsFilterExpression): Filter ' output_option['extra'] == 'FULL' or output_option['extra'] == 'DYNOMICS'' is no valid expression: unexpected indent (, line 1 +OutputsFilterExpression): Filter ' output_option['extra'] == 'TSV' ' is no valid expression: unexpected indent (, line 1 +OutputsFilterExpression): Filter ' output_option['nohtml'] == False' is no valid expression: unexpected indent (, line 1 +OutputsFilterExpression): Filter ' output_option['no_logfile'] == False ' is no valid expression: unexpected indent (, line 1 +TestsCaseValidation +TestsParamInInputs diff --git a/tools/repeatmasker/.lint_skip b/tools/repeatmasker/.lint_skip index 9b777a1b5b6..ac06880c07b 100644 --- a/tools/repeatmasker/.lint_skip +++ b/tools/repeatmasker/.lint_skip @@ -1,2 +1,3 @@ InputsNameRedundantArgument +TestsCaseValidation XMLOrder diff --git a/tools/repmatch_gff3/.lint_skip b/tools/repmatch_gff3/.lint_skip index cc60dd28c7b..9a302b99483 100644 --- a/tools/repmatch_gff3/.lint_skip +++ b/tools/repmatch_gff3/.lint_skip @@ -1 +1,2 @@ +TestsCaseValidation TestsExpectNumOutputs diff --git a/tools/revoluzer/.lint_skip b/tools/revoluzer/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/revoluzer/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/rgrnastar/.lint_skip b/tools/rgrnastar/.lint_skip new file mode 100644 index 00000000000..df8a3e5df45 --- /dev/null +++ b/tools/rgrnastar/.lint_skip @@ -0,0 +1,3 @@ +OutputsFilterExpression): Filter 'None' is no valid expression: compile( +TestsCaseValidation +TestsParamInInputs diff --git a/tools/rnaquast/.lint_skip b/tools/rnaquast/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/rnaquast/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/roary/.lint_skip b/tools/roary/.lint_skip index cc60dd28c7b..9a302b99483 100644 --- a/tools/roary/.lint_skip +++ b/tools/roary/.lint_skip @@ -1 +1,2 @@ +TestsCaseValidation TestsExpectNumOutputs diff --git a/tools/rp2biosensor/.lint_skip b/tools/rp2biosensor/.lint_skip index cc60dd28c7b..22aa3661fdc 100644 --- a/tools/rp2biosensor/.lint_skip +++ b/tools/rp2biosensor/.lint_skip @@ -1 +1,2 @@ +OutputsFilterExpression): Filter ' adv['json_graph'] ' is no valid expression: unexpected indent (, line 1 TestsExpectNumOutputs diff --git a/tools/rpbasicdesign/.lint_skip b/tools/rpbasicdesign/.lint_skip new file mode 100644 index 00000000000..ad6b30a6cc5 --- /dev/null +++ b/tools/rpbasicdesign/.lint_skip @@ -0,0 +1,2 @@ +OutputsFilterExpression): Filter ' adv['sbol_output'] ' is no valid expression: unexpected indent (, line 1 +TestsCaseValidation diff --git a/tools/rseqc/.lint_skip b/tools/rseqc/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/rseqc/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/ruvseq/.lint_skip b/tools/ruvseq/.lint_skip index ee3065a51c9..40ae0aea8c7 100644 --- a/tools/ruvseq/.lint_skip +++ b/tools/ruvseq/.lint_skip @@ -1,2 +1,3 @@ +TestsCaseValidation TestsExpectNumOutputs XMLOrder diff --git a/tools/sbml2sbol/.lint_skip b/tools/sbml2sbol/.lint_skip index 46f5e08e85b..a5aef4c7624 100644 --- a/tools/sbml2sbol/.lint_skip +++ b/tools/sbml2sbol/.lint_skip @@ -1 +1,2 @@ CitationsMissing +TestsCaseValidation diff --git a/tools/scanpy/.lint_skip b/tools/scanpy/.lint_skip new file mode 100644 index 00000000000..cd5da749677 --- /dev/null +++ b/tools/scanpy/.lint_skip @@ -0,0 +1,2 @@ +OutputsFilterExpression): Filter ' method['method'] == 'tl.rank_genes_groups' and method['get_df']['get_df_select'] == 'True'' is no valid expression: unexpected indent (, line 1 +TestsCaseValidation diff --git a/tools/scater/.lint_skip b/tools/scater/.lint_skip index 9b777a1b5b6..ac06880c07b 100644 --- a/tools/scater/.lint_skip +++ b/tools/scater/.lint_skip @@ -1,2 +1,3 @@ InputsNameRedundantArgument +TestsCaseValidation XMLOrder diff --git a/tools/sceasy/.lint_skip b/tools/sceasy/.lint_skip new file mode 100644 index 00000000000..4835fb975a3 --- /dev/null +++ b/tools/sceasy/.lint_skip @@ -0,0 +1,2 @@ +OutputsFilterExpression +TestsCaseValidation diff --git a/tools/scoary/.lint_skip b/tools/scoary/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/scoary/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/scpipe/.lint_skip b/tools/scpipe/.lint_skip index cc60dd28c7b..9a302b99483 100644 --- a/tools/scpipe/.lint_skip +++ b/tools/scpipe/.lint_skip @@ -1 +1,2 @@ +TestsCaseValidation TestsExpectNumOutputs diff --git a/tools/seacr/.lint_skip b/tools/seacr/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/seacr/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/semibin/.lint_skip b/tools/semibin/.lint_skip new file mode 100644 index 00000000000..156f092488f --- /dev/null +++ b/tools/semibin/.lint_skip @@ -0,0 +1,3 @@ +TestsCaseValidation +TestsCaseValidation): Serious problem parsing tool source or tests - cannot validate test cases. The exception is [invalid literal for int( +TestsParamInInputs diff --git a/tools/seqkit/.lint_skip b/tools/seqkit/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/seqkit/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/seqprep/.lint_skip b/tools/seqprep/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/seqprep/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/seqsero2/.lint_skip b/tools/seqsero2/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/seqsero2/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/seqtk/.lint_skip b/tools/seqtk/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/seqtk/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/seurat/.lint_skip b/tools/seurat/.lint_skip new file mode 100644 index 00000000000..f530e93cdd0 --- /dev/null +++ b/tools/seurat/.lint_skip @@ -0,0 +1,2 @@ +TestsCaseValidation +TestsParamInInputs diff --git a/tools/shasta/.lint_skip b/tools/shasta/.lint_skip new file mode 100644 index 00000000000..f530e93cdd0 --- /dev/null +++ b/tools/shasta/.lint_skip @@ -0,0 +1,2 @@ +TestsCaseValidation +TestsParamInInputs diff --git a/tools/shorah/.lint_skip b/tools/shorah/.lint_skip index ee3065a51c9..40ae0aea8c7 100644 --- a/tools/shorah/.lint_skip +++ b/tools/shorah/.lint_skip @@ -1,2 +1,3 @@ +TestsCaseValidation TestsExpectNumOutputs XMLOrder diff --git a/tools/shovill/.lint_skip b/tools/shovill/.lint_skip new file mode 100644 index 00000000000..dead302b400 --- /dev/null +++ b/tools/shovill/.lint_skip @@ -0,0 +1,2 @@ +OutputsFilterExpression): Filter ' adv['keep_files']['nocorr'] == 'yes_correction' and adv['keep_files']['keepfiles'] == True ' is no valid expression: unexpected indent (, line 1 +TestsCaseValidation diff --git a/tools/sickle/.lint_skip b/tools/sickle/.lint_skip index 561ac4b4543..319d7dc3a97 100644 --- a/tools/sickle/.lint_skip +++ b/tools/sickle/.lint_skip @@ -1,2 +1,3 @@ OutputsLabelDuplicatedFilter +TestsCaseValidation TestsExpectNumOutputs diff --git a/tools/simtext/.lint_skip b/tools/simtext/.lint_skip index e7d00398ee9..3f2477ee723 100644 --- a/tools/simtext/.lint_skip +++ b/tools/simtext/.lint_skip @@ -1 +1,2 @@ InputsNameRedundantArgument +TestsCaseValidation diff --git a/tools/sina/.lint_skip b/tools/sina/.lint_skip index ee3065a51c9..40ae0aea8c7 100644 --- a/tools/sina/.lint_skip +++ b/tools/sina/.lint_skip @@ -1,2 +1,3 @@ +TestsCaseValidation TestsExpectNumOutputs XMLOrder diff --git a/tools/sinto/.lint_skip b/tools/sinto/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/sinto/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/slamdunk/.lint_skip b/tools/slamdunk/.lint_skip index e7d00398ee9..3f2477ee723 100644 --- a/tools/slamdunk/.lint_skip +++ b/tools/slamdunk/.lint_skip @@ -1 +1,2 @@ InputsNameRedundantArgument +TestsCaseValidation diff --git a/tools/sleuth/.lint_skip b/tools/sleuth/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/sleuth/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/smudgeplot/.lint_skip b/tools/smudgeplot/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/smudgeplot/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/snapatac2/.lint_skip b/tools/snapatac2/.lint_skip new file mode 100644 index 00000000000..f530e93cdd0 --- /dev/null +++ b/tools/snapatac2/.lint_skip @@ -0,0 +1,2 @@ +TestsCaseValidation +TestsParamInInputs diff --git a/tools/sniffles/.lint_skip b/tools/sniffles/.lint_skip new file mode 100644 index 00000000000..f530e93cdd0 --- /dev/null +++ b/tools/sniffles/.lint_skip @@ -0,0 +1,2 @@ +TestsCaseValidation +TestsParamInInputs diff --git a/tools/snipit/.lint_skip b/tools/snipit/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/snipit/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/snippy/.lint_skip b/tools/snippy/.lint_skip index e6389d1e57b..aa2356bcc77 100644 --- a/tools/snippy/.lint_skip +++ b/tools/snippy/.lint_skip @@ -1,3 +1,4 @@ ConditionalParamTypeBool +TestsCaseValidation TestsExpectNumOutputs XMLOrder diff --git a/tools/snp-sites/.lint_skip b/tools/snp-sites/.lint_skip new file mode 100644 index 00000000000..f530e93cdd0 --- /dev/null +++ b/tools/snp-sites/.lint_skip @@ -0,0 +1,2 @@ +TestsCaseValidation +TestsParamInInputs diff --git a/tools/snpeff-covid19/.lint_skip b/tools/snpeff-covid19/.lint_skip index 38682cfa50a..9a79533a3d5 100644 --- a/tools/snpeff-covid19/.lint_skip +++ b/tools/snpeff-covid19/.lint_skip @@ -1,3 +1,4 @@ +TestsCaseValidation TestsExpectNumOutputs ToolVersionPEP404 XMLOrder diff --git a/tools/sonneityping/.lint_skip b/tools/sonneityping/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/sonneityping/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/spades/.lint_skip b/tools/spades/.lint_skip new file mode 100644 index 00000000000..f530e93cdd0 --- /dev/null +++ b/tools/spades/.lint_skip @@ -0,0 +1,2 @@ +TestsCaseValidation +TestsParamInInputs diff --git a/tools/spapros/.lint_skip b/tools/spapros/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/spapros/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/spotyping/.lint_skip b/tools/spotyping/.lint_skip index a68d017209e..1f78d73fa84 100644 --- a/tools/spotyping/.lint_skip +++ b/tools/spotyping/.lint_skip @@ -1 +1,2 @@ +TestsCaseValidation XMLOrder diff --git a/tools/sra-tools/.lint_skip b/tools/sra-tools/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/sra-tools/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/stacks/.lint_skip b/tools/stacks/.lint_skip index cc60dd28c7b..fd71d66f811 100644 --- a/tools/stacks/.lint_skip +++ b/tools/stacks/.lint_skip @@ -1 +1,3 @@ +TestsCaseValidation +TestsCaseValidation): Serious problem parsing tool source or tests - cannot validate test cases. The exception is [Invalid conditional test value (false) for parameter (genomic TestsExpectNumOutputs diff --git a/tools/stacks2/.lint_skip b/tools/stacks2/.lint_skip index 3f36fbca6c2..77e8d19cc41 100644 --- a/tools/stacks2/.lint_skip +++ b/tools/stacks2/.lint_skip @@ -1,3 +1,4 @@ CommandTODO InputsNameRedundantArgument OutputsLabelDuplicatedFilter +TestsCaseValidation diff --git a/tools/star_fusion/.lint_skip b/tools/star_fusion/.lint_skip index e7d00398ee9..3f2477ee723 100644 --- a/tools/star_fusion/.lint_skip +++ b/tools/star_fusion/.lint_skip @@ -1 +1,2 @@ InputsNameRedundantArgument +TestsCaseValidation diff --git a/tools/straindesign/.lint_skip b/tools/straindesign/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/straindesign/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/strelka/.lint_skip b/tools/strelka/.lint_skip index e7d00398ee9..3f2477ee723 100644 --- a/tools/strelka/.lint_skip +++ b/tools/strelka/.lint_skip @@ -1 +1,2 @@ InputsNameRedundantArgument +TestsCaseValidation diff --git a/tools/stringtie/.lint_skip b/tools/stringtie/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/stringtie/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/swift/.lint_skip b/tools/swift/.lint_skip index c4d48dac9f2..054aabe7163 100644 --- a/tools/swift/.lint_skip +++ b/tools/swift/.lint_skip @@ -1,2 +1,3 @@ InputsNameRedundantArgument +TestsCaseValidation TestsExpectNumOutputs diff --git a/tools/table_compute/.lint_skip b/tools/table_compute/.lint_skip index b5212db9362..6eca65e6374 100644 --- a/tools/table_compute/.lint_skip +++ b/tools/table_compute/.lint_skip @@ -1,2 +1,3 @@ CitationsNoValid +TestsCaseValidation): Serious problem parsing tool source or tests - cannot validate test cases. The exception is [Invalid conditional test value (All) for parameter (element_op TestsExpectNumOutputsFailing diff --git a/tools/tasmanian_mismatch/.lint_skip b/tools/tasmanian_mismatch/.lint_skip index cc60dd28c7b..9a302b99483 100644 --- a/tools/tasmanian_mismatch/.lint_skip +++ b/tools/tasmanian_mismatch/.lint_skip @@ -1 +1,2 @@ +TestsCaseValidation TestsExpectNumOutputs diff --git a/tools/taxonomy_filter_refseq/.lint_skip b/tools/taxonomy_filter_refseq/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/taxonomy_filter_refseq/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/taxonomy_krona_chart/.lint_skip b/tools/taxonomy_krona_chart/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/taxonomy_krona_chart/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/tb-profiler/.lint_skip b/tools/tb-profiler/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/tb-profiler/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/te_finder/.lint_skip b/tools/te_finder/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/te_finder/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/tn93/.lint_skip b/tools/tn93/.lint_skip index 232ad9b2230..c1e9c99d9b3 100644 --- a/tools/tn93/.lint_skip +++ b/tools/tn93/.lint_skip @@ -1,2 +1,3 @@ HelpInvalidRST OutputsLabelDuplicatedFilter +TestsCaseValidation diff --git a/tools/tooldistillator/.lint_skip b/tools/tooldistillator/.lint_skip new file mode 100644 index 00000000000..5c9fa5d36d6 --- /dev/null +++ b/tools/tooldistillator/.lint_skip @@ -0,0 +1 @@ +OutputsFilterExpression): Filter ' log == True ' is no valid expression: unexpected indent (, line 1 diff --git a/tools/tracegroomer/.lint_skip b/tools/tracegroomer/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/tracegroomer/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/transit/.lint_skip b/tools/transit/.lint_skip index a68d017209e..1f78d73fa84 100644 --- a/tools/transit/.lint_skip +++ b/tools/transit/.lint_skip @@ -1 +1,2 @@ +TestsCaseValidation XMLOrder diff --git a/tools/transtermhp/.lint_skip b/tools/transtermhp/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/transtermhp/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/trimal/.lint_skip b/tools/trimal/.lint_skip new file mode 100644 index 00000000000..75c7b591378 --- /dev/null +++ b/tools/trimal/.lint_skip @@ -0,0 +1,3 @@ +OutputsFilterExpression): Filter ' statistics ' is no valid expression: unexpected indent (, line 1 +OutputsFilterExpression): Filter ' trimming_mode['mode_selector'] != 'manual' ' is no valid expression: unexpected indent (, line 1 +TestsCaseValidation diff --git a/tools/trimmomatic/.lint_skip b/tools/trimmomatic/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/trimmomatic/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/trinity/.lint_skip b/tools/trinity/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/trinity/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/trycycler/.lint_skip b/tools/trycycler/.lint_skip new file mode 100644 index 00000000000..f530e93cdd0 --- /dev/null +++ b/tools/trycycler/.lint_skip @@ -0,0 +1,2 @@ +TestsCaseValidation +TestsParamInInputs diff --git a/tools/tximport/.lint_skip b/tools/tximport/.lint_skip index a68d017209e..1f78d73fa84 100644 --- a/tools/tximport/.lint_skip +++ b/tools/tximport/.lint_skip @@ -1 +1,2 @@ +TestsCaseValidation XMLOrder diff --git a/tools/ucsc_blat/.lint_skip b/tools/ucsc_blat/.lint_skip index a1cf37844af..846dc17ee85 100644 --- a/tools/ucsc_blat/.lint_skip +++ b/tools/ucsc_blat/.lint_skip @@ -1 +1,2 @@ +TestsCaseValidation): Serious problem parsing tool source or tests - cannot validate test cases. The exception is [invalid literal for int( TestsOutputCompareAttrib diff --git a/tools/ucsc_tools/fasplit/.lint_skip b/tools/ucsc_tools/fasplit/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/ucsc_tools/fasplit/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/ucsc_tools/maftoaxt/.lint_skip b/tools/ucsc_tools/maftoaxt/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/ucsc_tools/maftoaxt/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/umi_tools/.lint_skip b/tools/umi_tools/.lint_skip new file mode 100644 index 00000000000..f530e93cdd0 --- /dev/null +++ b/tools/umi_tools/.lint_skip @@ -0,0 +1,2 @@ +TestsCaseValidation +TestsParamInInputs diff --git a/tools/unicycler/.lint_skip b/tools/unicycler/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/unicycler/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/usher/.lint_skip b/tools/usher/.lint_skip new file mode 100644 index 00000000000..cbce9879e5e --- /dev/null +++ b/tools/usher/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation): Serious problem parsing tool source or tests - cannot validate test cases. The exception is [Invalid conditional test value (clades) for parameter (operation diff --git a/tools/varvamp/.lint_skip b/tools/varvamp/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/varvamp/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/vcf2maf/.lint_skip b/tools/vcf2maf/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/vcf2maf/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/vegan/.lint_skip b/tools/vegan/.lint_skip new file mode 100644 index 00000000000..1f5591904b0 --- /dev/null +++ b/tools/vegan/.lint_skip @@ -0,0 +1,2 @@ +TestsCaseValidation +TestsCaseValidation): Serious problem parsing tool source or tests - cannot validate test cases. The exception is [invalid literal for int( diff --git a/tools/velvet/.lint_skip b/tools/velvet/.lint_skip index a68d017209e..c85c54905b9 100644 --- a/tools/velvet/.lint_skip +++ b/tools/velvet/.lint_skip @@ -1 +1,3 @@ +TestsCaseValidation +TestsParamInInputs XMLOrder diff --git a/tools/verkko/.lint_skip b/tools/verkko/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/verkko/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/virheat/.lint_skip b/tools/virheat/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/virheat/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/volcanoplot/.lint_skip b/tools/volcanoplot/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/volcanoplot/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/vsearch/.lint_skip b/tools/vsearch/.lint_skip index de4e58e9ed1..074709d2465 100644 --- a/tools/vsearch/.lint_skip +++ b/tools/vsearch/.lint_skip @@ -1,3 +1,5 @@ InputsSelectOptionDuplicateText +TestsCaseValidation +TestsCaseValidation): Serious problem parsing tool source or tests - cannot validate test cases. The exception is [invalid literal for int( TestsExpectNumOutputs XMLOrder diff --git a/tools/vsnp/.lint_skip b/tools/vsnp/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/vsnp/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/weblogo3/.lint_skip b/tools/weblogo3/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/weblogo3/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/windowmasker/.lint_skip b/tools/windowmasker/.lint_skip new file mode 100644 index 00000000000..2092d1d0d68 --- /dev/null +++ b/tools/windowmasker/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/winnowmap/.lint_skip b/tools/winnowmap/.lint_skip index e7d00398ee9..f32b6aceaea 100644 --- a/tools/winnowmap/.lint_skip +++ b/tools/winnowmap/.lint_skip @@ -1 +1,3 @@ InputsNameRedundantArgument +OutputsFilterExpression): Filter 'None' is no valid expression: compile( +TestsCaseValidation diff --git a/tools/yahs/.lint_skip b/tools/yahs/.lint_skip new file mode 100644 index 00000000000..af6cd2f97d7 --- /dev/null +++ b/tools/yahs/.lint_skip @@ -0,0 +1,3 @@ +OutputsFilterExpression): Filter ' function['function_select'] == "yahs"' is no valid expression: unexpected indent (, line 1 +TestsCaseValidation +TestsParamInInputs