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concoct use bai from metadata #8007

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c397b1f
concoct: use bai from metadata
bernt-matthias May 20, 2026
393677e
concoct fix linter errors
bernt-matthias May 20, 2026
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1 change: 0 additions & 1 deletion tools/concoct/.lint_skip
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12 changes: 6 additions & 6 deletions tools/concoct/concoct.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -70,11 +70,11 @@ concoct
<param name="total_percentage_pca" value="100"/>
<param name="seed" value="1"/>
<param name="iterations" value="500"/>
<param name="no_cov_normalization" value=""/>
<param name="no_cov_normalization" value="false"/>
</section>
<section name="output">
<param name="no_total_coverage" value=""/>
<param name="converge_out" value=""/>
<param name="no_total_coverage" value="false"/>
<param name="converge_out" value="false"/>
<param name="log" value="true"/>
</section>
<output name="process_log" ftype="txt" compare="contains">
Expand Down Expand Up @@ -113,11 +113,11 @@ concoct
<param name="total_percentage_pca" value="100"/>
<param name="seed" value="1"/>
<param name="iterations" value="500"/>
<param name="no_cov_normalization" value=""/>
<param name="no_cov_normalization" value="false"/>
</section>
<section name="output">
<param name="no_total_coverage" value=""/>
<param name="converge_out" value=""/>
<param name="no_total_coverage" value="false"/>
<param name="converge_out" value="false"/>
<param name="log" value="false"/>
</section>
<output name="output_pca_components" ftype="csv">
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10 changes: 4 additions & 6 deletions tools/concoct/concoct_coverage_table.xml
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Expand Up @@ -10,15 +10,13 @@
mkdir 'mapping' &&
#if $mode.type == 'individual'
#set $identifier = re.sub('[^\s\w\-\\.]', '_', str($mode.bamfile))
ln -s '$mode.bamfile' 'mapping/${identifier}.sorted.bam' &&
samtools index 'mapping/${identifier}.sorted.bam' 'mapping/${identifier}.bam.bai' &&
mv 'mapping/${identifier}.sorted.bam' 'mapping/${identifier}.bam' &&
ln -s '$mode.bamfile' 'mapping/${identifier}.bam' &&
ln -s '$mode.bamfile.metadata.bam_index' 'mapping/${identifier}.bam.bai'
#else
#for $e in $mode.bamfiles
#set $identifier = re.sub('[^\s\w\-\\.]', '_', str($e.element_identifier))
ln -s '$e' 'mapping/${identifier}.sorted.bam' &&
samtools index 'mapping/${identifier}.sorted.bam' 'mapping/${identifier}.bam.bai' &&
mv 'mapping/${identifier}.sorted.bam' 'mapping/${identifier}.bam' &&
ln -s '$e' 'mapping/${identifier}.bam' &&
ln -s '$e.metadata.bam_index' 'mapping/${identifier}.bam.bai' &&
#end for
#end if
concoct_coverage_table.py
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6 changes: 3 additions & 3 deletions tools/concoct/cut_up_fasta.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -42,7 +42,7 @@ cut_up_fasta.py
<param name="input_fasta" value="two_contigs.fa"/>
<param name="chunk_size" value="1000" />
<param name="overlap_size" value="0"/>
<param name="merge_last" value=""/>
<param name="merge_last" value="false"/>
<param name="bedfile" value="false"/>
<output name="output_fasta" ftype="fasta">
<assert_contents>
Expand All @@ -57,7 +57,7 @@ cut_up_fasta.py
<param name="input_fasta" value="two_contigs.fa"/>
<param name="chunk_size" value="1000" />
<param name="overlap_size" value="0"/>
<param name="merge_last" value="--merge_last"/>
<param name="merge_last" value="true"/>
<param name="bedfile" value="true"/>
<output name="output_bed" ftype="bed">
<assert_contents>
Expand All @@ -79,7 +79,7 @@ cut_up_fasta.py
<param name="input_fasta" value="composition.fa.gz" ftype="fasta.gz"/>
<param name="chunk_size" value="500" />
<param name="overlap_size" value="499"/>
<param name="merge_last" value=""/>
<param name="merge_last" value="false"/>
<param name="bedfile" value="false"/>
<output name="output_fasta" ftype="fasta">
<assert_contents>
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