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Bugfix/sorting bam files #18

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Bugfix/sorting bam files #18

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8b86406
fixed issue in 03_index that required a sorted bam file before indexing
JenniferNeumaier Apr 9, 2026
9f1fcd0
added fix to handle automatic sorting of bam files were created by ST…
JenniferNeumaier Apr 10, 2026
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20 changes: 16 additions & 4 deletions modules/02_star.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,7 @@ process STAR {

script:
two_pass_mode_param = params.star_two_pass_mode ? "--twopassMode Basic" : ""
sort = params.star_sort_by_coordinate ? "SortedByCoordinate" : ""
sort = params.star_sort_by_coordinate ? "SortedByCoordinate" : "Unsorted"
"""
STAR --genomeDir ${reference} ${two_pass_mode_param} ${params.additional_args} \
--readFilesCommand "gzip -d -c -f" \
Expand All @@ -32,7 +32,13 @@ process STAR {
--runThreadN ${task.cpus} \
--outFileNamePrefix ${name}.

mv ${name}.Aligned*.out.bam ${name}.bam
# Handle sorting conditionally
if [ "${sort}" = "Unsorted" ]; then
samtools sort -@ ${task.cpus} -o ${name}.Aligned.SamtoolsSorted.out.bam ${name}.Aligned.out.bam
mv ${name}.Aligned.SamtoolsSorted.out.bam ${name}.bam
else
mv ${name}.Aligned.sortedByCoord.out.bam ${name}.bam
fi

echo ${params.manifest} >> software_versions.STAR.txt
STAR --version >> software_versions.STAR.txt
Expand All @@ -58,7 +64,7 @@ process STAR_SE {

script:
two_pass_mode_param = params.star_two_pass_mode ? "--twopassMode Basic" : ""
sort = params.star_sort_by_coordinate ? "SortedByCoordinate" : ""
sort = params.star_sort_by_coordinate ? "SortedByCoordinate" : "Unsorted"
"""
STAR --genomeDir ${reference} ${two_pass_mode_param} ${params.additional_args} \
--readFilesCommand "gzip -d -c -f" \
Expand All @@ -72,7 +78,13 @@ process STAR_SE {
--runThreadN ${task.cpus} \
--outFileNamePrefix ${name}.

mv ${name}.Aligned*.out.bam ${name}.bam
# Handle sorting conditionally
if [ "${sort}" = "Unsorted" ]; then
samtools sort -@ ${task.cpus} -o ${name}.Aligned.SamtoolsSorted.out.bam ${name}.Aligned.out.bam
mv ${name}.Aligned.SamtoolsSorted.out.bam ${name}.bam
else
mv ${name}.Aligned.sortedByCoord.out.bam ${name}.bam
fi

echo ${params.manifest} >> software_versions.STAR_SE.txt
STAR --version >> software_versions.STAR_SE.txt
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2 changes: 1 addition & 1 deletion modules/03_index.nf
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Expand Up @@ -21,4 +21,4 @@ process INDEX_BAM {
echo ${params.manifest} >> software_versions.INDEX_BAM.txt
samtools --version >> software_versions.INDEX_BAM.txt
"""
}
}
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