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HISAT2.wdl: replace output command substitutions with explicit fifo/wait #233

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HISAT2.wdl: replace output command substitutions with explicit fifo/wait #233

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e9f5177
HISAT2.wdl: replace output command substitutions with explicit fifo/wait
mlin Jul 18, 2019
e225018
[squash] fix typo
mlin Jul 18, 2019
5b2264e
Merge branch 'master' into mlin-hisat2-command-sub
mlin Nov 13, 2019
fa7524a
Merge branch 'master' into mlin-hisat2-command-sub
nikellepetrillo Jul 20, 2020
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20 changes: 16 additions & 4 deletions library/tasks/HISAT2.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -62,6 +62,8 @@ task HISAT2PairedEnd {
# --seed to fix pseudo-random number and in order to produce deterministics results
# --secondary reports secondary alignments for multimapping reads. -k 10
# searches for up to 10 primary alignments for each read
mkfifo samtools_pipe
samtools view -1 -h -o "${output_basename}_unsorted.bam" samtools_pipe & pid=$!
hisat2 -t \
-x ${ref_name}/${ref_name} \
-1 $FQ1 \
Expand All @@ -73,7 +75,8 @@ task HISAT2PairedEnd {
--seed 12345 \
-k 10 \
--secondary \
-p ${cpu} -S >(samtools view -1 -h -o ${output_basename}_unsorted.bam)
-p ${cpu} -S samtools_pipe
wait $pid
samtools sort -@ ${cpu} -O bam -o "${output_basename}.bam" "${output_basename}_unsorted.bam"
samtools index "${output_basename}.bam"
}
Expand Down Expand Up @@ -158,6 +161,8 @@ task HISAT2RSEM {
# with no-splice-alignment no-softclip no-mixed options on, HISAT2 will only output concordant alignment without soft-cliping
# --rdg 99999999,99999999 and --rfg 99999999,99999999 will set an infinite penalty to alignments with indels.
# As a result, alignments with gaps or deletions are excluded.
mkfifo samtools_pipe
samtools view -1 -h -o "${output_basename}.bam" samtools_pipe & pid=$!
hisat2 -t \
-x ${ref_name}/${ref_name} \
-1 $FQ1 \
Expand All @@ -178,7 +183,8 @@ task HISAT2RSEM {
--rfg 99999999,99999999 \
--no-spliced-alignment \
--seed 12345 \
-p ${cpu} -S >(samtools view -1 -h -o ${output_basename}.bam)
-p ${cpu} -S samtools_pipe
wait $pid
}

runtime {
Expand Down Expand Up @@ -236,6 +242,8 @@ task HISAT2SingleEnd {
tar --no-same-owner -xvf "${hisat2_ref}"

# The parameters for this task are copied from the HISAT2PairedEnd task.
mkfifo samtools_pipe
samtools view -1 -h -o "${output_basename}_unsorted.bam" samtools_pipe & pid=$!
hisat2 -t \
-x ${ref_name}/${ref_name} \
-U ${fastq} \
Expand All @@ -246,7 +254,8 @@ task HISAT2SingleEnd {
--seed 12345 \
-k 10 \
--secondary \
-p ${cpu} -S >(samtools view -1 -h -o ${output_basename}_unsorted.bam)
-p ${cpu} -S samtools_pipe
wait $pid
samtools sort -@ ${cpu} -O bam -o "${output_basename}.bam" "${output_basename}_unsorted.bam"
samtools index "${output_basename}.bam"
}
Expand Down Expand Up @@ -367,6 +376,8 @@ task HISAT2RSEMSingleEnd {
# with no-splice-alignment no-softclip no-mixed options on, HISAT2 will only output concordant alignment without soft-cliping
# --rdg 99999999,99999999 and --rfg 99999999,99999999 will set an infinite penalty to alignments with indels.
# As a result, alignments with gaps or deletions are excluded.
mkfifo samtools_pipe
samtools view -1 -h -o "${output_basename}.bam" samtools_pipe & pid=$!
hisat2 -t \
-x ${ref_name}/${ref_name} \
-U $FQ \
Expand All @@ -386,7 +397,8 @@ task HISAT2RSEMSingleEnd {
--rfg 99999999,99999999 \
--no-spliced-alignment \
--seed 12345 \
-p ${cpu} -S >(samtools view -1 -h -o ${output_basename}.bam)
-p ${cpu} -S samtools_pipe
wait $pid
}

runtime {
Expand Down