Add tags showing sample_id

Former-commit-id: f9bc941

modules/amr.nf

@@ -2,6 +2,8 @@
 process PBP_RESISTANCE {
     label 'spn_pbp_amr_container'
 
+    tag "$sample_id"
+
     input:
     tuple val(sample_id), path(assembly)
 
@@ -21,6 +23,8 @@ process PBP_RESISTANCE {
 process GET_PBP_RESISTANCE {
     label 'bash_container'
 
+    tag "$sample_id"
+
     input:
     tuple val(sample_id), path(json)
 
@@ -64,6 +68,8 @@ process GET_PBP_RESISTANCE {
 process OTHER_RESISTANCE {
     label 'amrsearch_container'
 
+    tag "$sample_id"
+
     input:
     tuple val(sample_id), path(assembly)
 
@@ -80,6 +86,8 @@ process OTHER_RESISTANCE {
 process GET_OTHER_RESISTANCE {
     label 'bash_container'
 
+    tag "$sample_id"
+
     input:
     tuple val(sample_id), path(json)
 

modules/assembly.nf

@@ -4,6 +4,8 @@
 process ASSEMBLY_UNICYCLER {
     label 'unicycler_container'
 
+    tag "$sample_id"
+
     publishDir "$params.output/assemblies", mode: 'link'
 
     input:
@@ -24,6 +26,8 @@ process ASSEMBLY_UNICYCLER {
 process ASSEMBLY_SHOVILL {
     label 'shovill_container'
 
+    tag "$sample_id"
+
     publishDir "$params.output/assemblies", mode: 'link'
 
     input:
@@ -43,6 +47,8 @@ process ASSEMBLY_SHOVILL {
 process ASSEMBLY_ASSESS {
     label 'quast_container'
 
+    tag "$sample_id"
+
     input:
     tuple val(sample_id), path(assembly)
     output:
@@ -58,6 +64,8 @@ process ASSEMBLY_ASSESS {
 process ASSEMBLY_QC {
     label 'bash_container'
 
+    tag "$sample_id"
+
     input:
     tuple val(sample_id), path(report), val(bases)
     val(qc_contigs)

modules/lineage.nf

@@ -84,6 +84,8 @@ process GET_POPPUNK_EXT_CLUSTERS {
 process LINEAGE {
     label 'poppunk_container'
 
+    tag "All samples"
+
     input:
     tuple path(poppunk_dir), val(db_name)
     val ext_clusters_file

modules/mapping.nf

@@ -40,6 +40,8 @@ process GET_REF_GENOME_BWA_DB_PREFIX {
 process MAPPING {
     label 'bwa_container'
 
+    tag "$sample_id"
+
     input:
     tuple path(bwa_ref_db_dir), val(prefix)
     tuple val(sample_id), path(read1), path(read2), path(unpaired)
@@ -57,6 +59,8 @@ process MAPPING {
 // Return sorted BAM
 process SAM_TO_SORTED_BAM {
     label 'samtools_container'
+
+    tag "$sample_id"
 
     input:
     tuple val(sample_id), path(sam)
@@ -77,6 +81,8 @@ process SAM_TO_SORTED_BAM {
 // Return reference coverage percentage by the reads
 process REF_COVERAGE {
     label 'samtools_container'
+
+    tag "$sample_id"
 
     input:
     tuple val(sample_id), path(bam)
@@ -94,6 +100,8 @@ process REF_COVERAGE {
 // Return .vcf by calling the SNPs
 process SNP_CALL {
     label 'bcftools_container'
+
+    tag "$sample_id"
 
     input:
     path reference
@@ -112,6 +120,8 @@ process SNP_CALL {
 process HET_SNP_COUNT {
     label 'python_container'
 
+    tag "$sample_id"
+
     input:
     tuple val(sample_id), path(vcf)
 
@@ -128,6 +138,8 @@ process HET_SNP_COUNT {
 process MAPPING_QC {
     label 'bash_container'
 
+    tag "$sample_id"
+
     input:
     tuple val(sample_id), val(ref_coverage), val(het_snp_count)
     val(qc_ref_coverage)

modules/mlst.nf

@@ -2,6 +2,8 @@
 process MLST {
     label 'mlst_container'
 
+    tag "$sample_id"
+
     input:
     tuple val(sample_id), path(assembly)
 

modules/overall_qc.nf

@@ -1,6 +1,8 @@
 // Return overall QC result based on Assembly QC, Mapping QC and Taxonomy QC
 process OVERALL_QC {
     label 'bash_container'
+
+    tag "$sample_id"
 
     input:
     tuple val(sample_id), val(ASSEMBLY_QC), val(MAPPING_QC), val(TAXONOMY_QC)

modules/preprocess.nf

@@ -2,6 +2,8 @@
 process PREPROCESS {
     label 'fastp_container'
 
+    tag "$sample_id"
+
     input:
     tuple val(sample_id), path(reads)
 
@@ -19,6 +21,8 @@ process PREPROCESS {
 process GET_BASES {
     label 'bash_container'
 
+    tag "$sample_id"
+
     input:
     tuple val(sample_id), path(json)
 

modules/serotype.nf

@@ -65,6 +65,8 @@ process CREATE_SEROBA_DB {
 process SEROTYPE {
     label 'seroba_container'
 
+    tag "$sample_id"
+
     input:
     tuple path(seroba_dir), val(database)
     tuple val(sample_id), path(read1), path(read2), path(unpaired)

modules/taxonomy.nf

@@ -40,6 +40,8 @@ process GET_KRAKEN_DB {
 process TAXONOMY {
     label 'kraken2_container'
 
+    tag "$sample_id"
+
     input:
     path kraken_db
     val kraken2_memory_mapping
@@ -63,6 +65,8 @@ process TAXONOMY {
 process TAXONOMY_QC {
     label 'bash_container'
 
+    tag "$sample_id"
+
     input:
     tuple val(sample_id), path(kraken_report)
     val(qc_spneumo_percentage)