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Use CRAM reference in samtools commands #236

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Use CRAM reference in samtools commands #236

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7 changes: 4 additions & 3 deletions modules/local/common.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -722,6 +722,7 @@ process extract_not_haplotagged_contigs {
cpus 8
memory 8.GB
input:
tuple path(ref), path(ref_idx), path(ref_cache), env(REF_PATH)
tuple path(xam), path(xam_idx), val(xam_meta)
path("haplotagged_sq.fosn")
output:
Expand All @@ -732,7 +733,7 @@ process extract_not_haplotagged_contigs {
mkdir -p output

# create file of sequence names by extracting all SQ SN
samtools view -H --no-PG '${xam}' | grep '^@SQ' | sed -nE 's,.*SN:([^[:space:]]*).*,\\1,p' > all_sq.fosn
samtools view -r '${ref}' -H --no-PG '${xam}' | grep '^@SQ' | sed -nE 's,.*SN:([^[:space:]]*).*,\\1,p' > all_sq.fosn

# pull out contigs that do not appear in the haplotagged fofn
# sort haplotagged contig list here (dont leave it to nextflow collectfile)
Expand All @@ -741,14 +742,14 @@ process extract_not_haplotagged_contigs {
if [ -s unhaplotagged_sq.fosn ]; then
while read sq; do
echo "Extracting \${sq}"
samtools view ${xam} "\${sq}" -@ ${extra_view_threads} --no-PG -o "output/\${sq}_nohp.bam"
samtools view -r '${ref}' ${xam} "\${sq}" -@ ${extra_view_threads} --no-PG -o "output/\${sq}_nohp.bam"
done < unhaplotagged_sq.fosn
fi

# bonus bam: pull out unaligned - this file will always be created
# use '*' region rather than -f4 for speeds
echo "Extracting *"
samtools view ${xam} '*' -@ ${extra_view_threads} --no-PG -o output/unaligned.bam
samtools view -r '${ref}' ${xam} '*' -@ ${extra_view_threads} --no-PG -o output/unaligned.bam
"""
}

2 changes: 1 addition & 1 deletion workflows/wf-human-snp.nf
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Expand Up @@ -193,7 +193,7 @@ workflow snp {
// chr, extracting all the decoys and unaligned reads is reasonably
// inexpensive. a small BED with high coverage may be less appropriate.
nothaplotagged_ctg_bams = \
extract_not_haplotagged_contigs(bam_channel, haplotagged_fosn)
extract_not_haplotagged_contigs(ref, bam_channel, haplotagged_fosn)
| transpose // squish to meet the expected shape for haplotagged_ctg_bams

xams_to_cat = \
Expand Down