diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index b62afb3d180bff6f476343673bb5996e3c42b8e4..e459b9a8fd2277f58190664cca4446185fd3bca5 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -79,7 +79,6 @@ process trackStart {
*/
process getBag {
tag "${repRID}"
- publishDir "${logsDir}", mode: "copy", pattern: "${repRID}.getBag.{out,err}"
input:
path credential, stageAs: "credential.json" from deriva
@@ -87,21 +86,20 @@ process getBag {
output:
path ("Replicate_*.zip") into bagit
- path ("${repRID}.getBag.err")
script:
"""
- hostname > ${repRID}.getBag.err
- ulimit -a >> ${repRID}.getBag.err
+ hostname > ${repRID}.getBag.log
+ ulimit -a >> ${repRID}.getBag.log
export https_proxy=\${http_proxy}
# link credential file for authentication
- ln -sf `readlink -e credential.json` ~/.deriva/credential.json 1>> ${repRID}.getBag.out 2>> ${repRID}.getBag.err
- echo "LOG: deriva credentials linked" >> ${repRID}.getBag.err
+ ln -sf `readlink -e credential.json` ~/.deriva/credential.json
+ echo "LOG: deriva credentials linked" >> ${repRID}.getBag.log
# deriva-download replicate RID
- echo "LOG: fetching deriva catalog for selected RID in GUDMAP." >> ${repRID}.getBag.err
- deriva-download-cli dev.gudmap.org --catalog 2 ${derivaConfig} . rid=${repRID} 1>> ${repRID}.getBag.out 2>> ${repRID}.getBag.err
+ echo "LOG: fetching deriva catalog for selected RID in GUDMAP." >> ${repRID}.getBag.log
+ deriva-download-cli dev.gudmap.org --catalog 2 ${derivaConfig} . rid=${repRID}
"""
}
@@ -110,7 +108,6 @@ process getBag {
*/
process getData {
tag "${repRID}"
- publishDir "${logsDir}", mode: "copy", pattern: "${repRID}.getData.{out,err}"
input:
path script_bdbagFetch
@@ -122,29 +119,28 @@ process getData {
path ("**/File.csv") into fileMeta
path ("**/Experiment Settings.csv") into experimentSettingsMeta
path ("**/Experiment.csv") into experimentMeta
- path ("${repRID}.getData.{out,err}")
script:
"""
- hostname > ${repRID}.getData.err
- ulimit -a >> ${repRID}.getData.err
+ hostname > ${repRID}.getData.log
+ ulimit -a >> ${repRID}.getData.log
export https_proxy=\${http_proxy}
# link deriva cookie for authentication
- ln -sf `readlink -e deriva-cookies.txt` ~/.bdbag/deriva-cookies.txt 1>> ${repRID}.getData.out 2>> ${repRID}.getData.err
- echo "LOG: deriva cookie linked" >> ${repRID}.getData.err
+ ln -sf `readlink -e deriva-cookies.txt` ~/.bdbag/deriva-cookies.txt
+ echo "LOG: deriva cookie linked" >> ${repRID}.getData.log
# get bagit basename
- replicate=\$(basename "${bagit}" | cut -d "." -f1) 1>> ${repRID}.getData.out 2>> ${repRID}.getData.err
- echo "LOG: \${replicate}" >> ${repRID}.getData.err
+ replicate=\$(basename "${bagit}" | cut -d "." -f1)
+ echo "LOG: \${replicate}" >> ${repRID}.getData.log
# unzip bagit
- unzip ${bagit} 1>> ${repRID}.getData.out 2>> ${repRID}.getData.err
- echo "LOG: replicate bdbag unzipped" >> ${repRID}.getData.err
+ unzip ${bagit}
+ echo "LOG: replicate bdbag unzipped" >> ${repRID}.getData.log
# bagit fetch fastq"s only and rename by repRID
- sh ${script_bdbagFetch} \${replicate} ${repRID} 1>> ${repRID}.getData.out 2>> ${repRID}.getData.err
- echo "LOG: replicate bdbag fetched" >> ${repRID}.getData.err
+ sh ${script_bdbagFetch} \${replicate} ${repRID}
+ echo "LOG: replicate bdbag fetched" >> ${repRID}.getData.log
"""
}
@@ -159,7 +155,6 @@ fastqs.into {
*/
process parseMetadata {
tag "${repRID}"
- publishDir "${logsDir}", mode: "copy", pattern: "${repRID}.parseMetadata.{out,err}"
input:
path script_parseMeta
@@ -169,44 +164,43 @@ process parseMetadata {
output:
path "design.csv" into metadata
- path "${repRID}.parseMetadata.{out,err}"
script:
"""
- hostname > ${repRID}.parseMetadata.err
- ulimit -a >> ${repRID}.parseMetadata.err
+ hostname > ${repRID}.parseMetadata.log
+ ulimit -a >> ${repRID}.parseMetadata.log
# check replicate RID metadata
rep=\$(python3 ${script_parseMeta} -r ${repRID} -m "${fileMeta}" -p repRID)
- echo "LOG: replicate RID metadata parsed: \${rep}" >> ${repRID}.parseMetadata.err
+ echo "LOG: replicate RID metadata parsed: \${rep}" >> ${repRID}.parseMetadata.log
# get experiment RID metadata
exp=\$(python3 ${script_parseMeta} -r ${repRID} -m "${fileMeta}" -p expRID)
- echo "LOG: experiment RID metadata parsed: \${exp}" >> ${repRID}.parseMetadata.err
+ echo "LOG: experiment RID metadata parsed: \${exp}" >> ${repRID}.parseMetadata.log
# get study RID metadata
study=\$(python3 ${script_parseMeta} -r ${repRID} -m "${fileMeta}" -p studyRID)
- echo "LOG: study RID metadata parsed: \${study}" >> ${repRID}.parseMetadata.err
+ echo "LOG: study RID metadata parsed: \${study}" >> ${repRID}.parseMetadata.log
# get endedness metadata
endsMeta=\$(python3 ${script_parseMeta} -r ${repRID} -m "${experimentSettingsMeta}" -p endsMeta)
- echo "LOG: endedness metadata parsed: \${endsMeta}" >> ${repRID}.parseMetadata.err
+ echo "LOG: endedness metadata parsed: \${endsMeta}" >> ${repRID}.parseMetadata.log
# ganually get endness
endsManual=\$(python3 ${script_parseMeta} -r ${repRID} -m "${fileMeta}" -p endsManual)
- echo "LOG: endedness manually detected: \${endsManual}" >> ${repRID}.parseMetadata.err
+ echo "LOG: endedness manually detected: \${endsManual}" >> ${repRID}.parseMetadata.log
# get strandedness metadata
stranded=\$(python3 ${script_parseMeta} -r ${repRID} -m "${experimentSettingsMeta}" -p stranded)
- echo "LOG: strandedness metadata parsed: \${stranded}" >> ${repRID}.parseMetadata.err
+ echo "LOG: strandedness metadata parsed: \${stranded}" >> ${repRID}.parseMetadata.log
# get spike-in metadata
spike=\$(python3 ${script_parseMeta} -r ${repRID} -m "${experimentSettingsMeta}" -p spike)
- echo "LOG: spike-in metadata parsed: \${spike}" >> ${repRID}.parseMetadata.err
+ echo "LOG: spike-in metadata parsed: \${spike}" >> ${repRID}.parseMetadata.log
# get species metadata
species=\$(python3 ${script_parseMeta} -r ${repRID} -m "${experimentMeta}" -p species)
- echo "LOG: species metadata parsed: \${species}" >> ${repRID}.parseMetadata.err
+ echo "LOG: species metadata parsed: \${species}" >> ${repRID}.parseMetadata.log
# gave design file
echo "\${endsMeta},\${endsManual},\${stranded},\${spike},\${species},\${exp},\${study}" > design.csv
@@ -244,7 +238,6 @@ endsManual.into {
*/
process trimData {
tag "${repRID}"
- publishDir "${logsDir}", mode: "copy", pattern: "${repRID}.trimData.{out,err}"
input:
val ends from endsManual_trimData
@@ -253,22 +246,21 @@ process trimData {
output:
path ("*.fq.gz") into fastqsTrim
path ("*_trimming_report.txt") into trimQC
- path ("${repRID}.trimData.{out,err}")
script:
"""
- hostname > ${repRID}.trimData.err
- ulimit -a >> ${repRID}.trimData.err
+ hostname > ${repRID}.trimData.log
+ ulimit -a >> ${repRID}.trimData.log
# trim fastq's using trim_galore
if [ "${ends}" == "se" ]
then
- echo "LOG: running trim_galore using single-end settings" >> ${repRID}.trimData.err
- trim_galore --gzip -q 25 --illumina --length 35 --basename ${repRID} -j `nproc` ${fastq[0]} 1>> ${repRID}.trimData.out 2>> ${repRID}.trimData.err
+ echo "LOG: running trim_galore using single-end settings" >> ${repRID}.trimData.log
+ trim_galore --gzip -q 25 --illumina --length 35 --basename ${repRID} -j `nproc` ${fastq[0]}
elif [ "${ends}" == "pe" ]
then
- echo "LOG: running trim_galore using paired-end settings" >> ${repRID}.trimData.err
- trim_galore --gzip -q 25 --illumina --length 35 --paired --basename ${repRID} -j `nproc` ${fastq[0]} ${fastq[1]} 1>> ${repRID}.trimData.out 2>> ${repRID}.trimData.err
+ echo "LOG: running trim_galore using paired-end settings" >> ${repRID}.trimData.log
+ trim_galore --gzip -q 25 --illumina --length 35 --paired --basename ${repRID} -j `nproc` ${fastq[0]} ${fastq[1]}
fi
"""
}
@@ -284,7 +276,6 @@ fastqsTrim.into {
*/
process getRefInfer {
tag "${refName}"
- publishDir "${logsDir}", mode: "copy", pattern: "${repRID}.getRefInfer.{out,err}"
input:
val refName from referenceInfer
@@ -292,12 +283,11 @@ process getRefInfer {
output:
tuple val (refName), path ("hisat2", type: 'dir'), path ("*.fna"), path ("*.gtf") into refInfer
path ("${refName}", type: 'dir') into bedInfer
- path ("${repRID}.getRefInfer.{out,err}")
script:
"""
- hostname > ${repRID}.getRefInfer.err
- ulimit -a >> ${repRID}.getRefInfer.err
+ hostname > ${repRID}.getRefInfer.log
+ ulimit -a >> ${repRID}.getRefInfer.log
export https_proxy=\${http_proxy}
# set the reference name
@@ -311,7 +301,7 @@ process getRefInfer {
then
references=\$(echo ${referenceBase}/GRCh${refHuVersion})
else
- echo -e "LOG: ERROR - References could not be set!\nReference found: ${referenceBase}" >> ${repRID}.getRefInfer.err
+ echo -e "LOG: ERROR - References could not be set!\nReference found: ${referenceBase}" >> ${repRID}.getRefInfer.log
exit 1
fi
mkdir ${refName}
@@ -319,18 +309,18 @@ process getRefInfer {
# retreive appropriate reference appropriate location
if [ ${referenceBase} == "s3://bicf-references" ]
then
- echo "LOG: grabbing reference files from S3" >> ${repRID}.getRefInfer.err
- aws s3 cp "\${references}" /hisat2 ./ --recursive 1>> ${repRID}.getRefInfer.out 2>> ${repRID}.getRefInfer.err
- aws s3 cp "\${references}" /bed ./${refName}/ --recursive 1>> ${repRID}.getRefInfer.out 2>> ${repRID}.getRefInfer.err
- aws s3 cp "\${references}" /*.fna --recursive 1>> ${repRID}.getRefInfer.out 2>> ${repRID}.getRefInfer.err
- aws s3 cp "\${references}" /*.gtf --recursive 1>> ${repRID}.getRefInfer.out 2>> ${repRID}.getRefInfer.err
+ echo "LOG: grabbing reference files from S3" >> ${repRID}.getRefInfer.log
+ aws s3 cp "\${references}" /hisat2 ./ --recursive
+ aws s3 cp "\${references}" /bed ./${refName}/ --recursive
+ aws s3 cp "\${references}" /*.fna --recursive
+ aws s3 cp "\${references}" /*.gtf --recursive
elif [ ${referenceBase} == "/project/BICF/BICF_Core/shared/gudmap/references" ]
then
- echo "LOG: using pre-defined locations for reference files" >> ${repRID}.getRefInfer.err
- ln -s "\${references}"/hisat2 1>> ${repRID}.getRefInfer.out 2>> ${repRID}.getRefInfer.err
- ln -s "\${references}"/bed ${refName}/bed 1>> ${repRID}.getRefInfer.out 2>> ${repRID}.getRefInfer.err
- ln -s "\${references}"/genome.fna 1>> ${repRID}.getRefInfer.out 2>> ${repRID}.getRefInfer.err
- ln -s "\${references}"/genome.gtf 1>> ${repRID}.getRefInfer.out 2>> ${repRID}.getRefInfer.err
+ echo "LOG: using pre-defined locations for reference files" >> ${repRID}.getRefInfer.log
+ ln -s "\${references}"/hisat2
+ ln -s "\${references}"/bed ${refName}/bed
+ ln -s "\${references}"/genome.fna
+ ln -s "\${references}"/genome.gtf
fi
# make blank bed folder for ERCC
@@ -347,7 +337,6 @@ process getRefInfer {
*/
process downsampleData {
tag "${repRID}"
- publishDir "${logsDir}", mode: "copy", pattern: "${repRID}.downsampleData.{out,err}"
input:
val ends from endsManual_downsampleData
@@ -356,25 +345,24 @@ process downsampleData {
output:
path ("sampled.1.fq") into fastqs1Sample
path ("sampled.2.fq") into fastqs2Sample
- path ("${repRID}.downsampleData.{out,err}")
script:
"""
- hostname > ${repRID}.downsampleData.err
- ulimit -a >> ${repRID}.downsampleData.err
+ hostname > ${repRID}.downsampleData.log
+ ulimit -a >> ${repRID}.downsampleData.log
export https_proxy=\${http_proxy}
if [ "${ends}" == "se" ]
then
- echo "LOG: downsampling single-end trimmed fastq" >> ${repRID}.downsampleData.err
- seqtk sample -s100 *trimmed.fq.gz 100000 1> sampled.1.fq 2>> ${repRID}.downsampleData.err
+ echo "LOG: downsampling single-end trimmed fastq" >> ${repRID}.downsampleData.log
+ seqtk sample -s100 *trimmed.fq.gz 100000 1> sampled.1.fq
touch sampled.2.fq
elif [ "${ends}" == "pe" ]
then
- echo "LOG: downsampling read 1 of paired-end trimmed fastq" >> ${repRID}.downsampleData.err
- seqtk sample -s100 *1.fq.gz 1000000 1> sampled.1.fq 2>> ${repRID}.downsampleData.err
- echo "LOG: downsampling read 2 of paired-end trimmed fastq" >> ${repRID}.downsampleData.err
- seqtk sample -s100 *2.fq.gz 1000000 1> sampled.2.fq 2>> ${repRID}.downsampleData.err
+ echo "LOG: downsampling read 1 of paired-end trimmed fastq" >> ${repRID}.downsampleData.log
+ seqtk sample -s100 *1.fq.gz 1000000 1> sampled.1.fq
+ echo "LOG: downsampling read 2 of paired-end trimmed fastq" >> ${repRID}.downsampleData.log
+ seqtk sample -s100 *2.fq.gz 1000000 1> sampled.2.fq
fi
"""
}
@@ -387,7 +375,6 @@ inferInput = endsManual_alignSampleData.combine(refInfer.combine(fastqs1Sample.c
*/
process alignSampleData {
tag "${ref}"
- publishDir "${logsDir}", mode: "copy", pattern: "${repRID}.alignSampleData.{out,err}"
input:
tuple val (ends), val (ref), path (hisat2), path (fna), path (gtf), path (fastq1), path (fastq2) from inferInput
@@ -396,35 +383,34 @@ process alignSampleData {
path ("${ref}.sampled.sorted.bam") into sampleBam
path ("${ref}.sampled.sorted.bam.bai") into sampleBai
path ("${ref}.alignSampleSummary.txt") into alignSampleQC
- path ("${repRID}.${ref}.alignSampleData.{out,err}")
script:
"""
- hostname > ${repRID}.${ref}.alignSampleData.err
- ulimit -a >> ${repRID}.${ref}.alignSampleData.err
+ hostname > ${repRID}.${ref}.alignSampleData.log
+ ulimit -a >> ${repRID}.${ref}.alignSampleData.log
# align the reads with Hisat 2
if [ "${ends}" == "se" ]
then
- echo "LOG: running Hisat2 with single-end settings" >> ${repRID}.${ref}.alignSampleData.err
- hisat2 -p `nproc` --add-chrname -S ${ref}.sampled.sam -x hisat2/genome -U ${fastq1} --summary-file ${ref}.alignSampleSummary.txt --new-summary 1>> ${repRID}.${ref}.alignSampleData.out 2>> ${repRID}.${ref}.alignSampleData.err
+ echo "LOG: running Hisat2 with single-end settings" >> ${repRID}.${ref}.alignSampleData.log
+ hisat2 -p `nproc` --add-chrname -S ${ref}.sampled.sam -x hisat2/genome -U ${fastq1} --summary-file ${ref}.alignSampleSummary.txt --new-summary
elif [ "${ends}" == "pe" ]
then
- echo "LOG: running Hisat2 with paired-end settings" >> ${repRID}.${ref}.alignSampleData.err
- hisat2 -p `nproc` --add-chrname -S ${ref}.sampled.sam -x hisat2/genome --no-mixed --no-discordant -1 ${fastq1} -2 ${fastq2} --summary-file ${ref}.alignSampleSummary.txt --new-summary 1>> ${repRID}.${ref}.alignSampleData.out 2>> ${repRID}.${ref}.alignSampleData.err
+ echo "LOG: running Hisat2 with paired-end settings" >> ${repRID}.${ref}.alignSampleData.log
+ hisat2 -p `nproc` --add-chrname -S ${ref}.sampled.sam -x hisat2/genome --no-mixed --no-discordant -1 ${fastq1} -2 ${fastq2} --summary-file ${ref}.alignSampleSummary.txt --new-summary
fi
# convert the output sam file to a sorted bam file using Samtools
- echo "LOG: converting from sam to bam" >> ${repRID}.${ref}.alignSampleData.err
- samtools view -1 -@ `nproc` -F 4 -F 8 -F 256 -o ${ref}.sampled.bam ${ref}.sampled.sam 1>> ${repRID}.${ref}.alignSampleData.out 2>> ${repRID}.${ref}.alignSampleData.err;
+ echo "LOG: converting from sam to bam" >> ${repRID}.${ref}.alignSampleData.log
+ samtools view -1 -@ `nproc` -F 4 -F 8 -F 256 -o ${ref}.sampled.bam ${ref}.sampled.sam
# sort the bam file using Samtools
- echo "LOG: sorting the bam file" >> ${repRID}.${ref}.alignSampleData.err
- samtools sort -@ `nproc` -O BAM -o ${ref}.sampled.sorted.bam ${ref}.sampled.bam 1>> ${repRID}.${ref}.alignSampleData.out 2>> ${repRID}.${ref}.alignSampleData.err;
+ echo "LOG: sorting the bam file" >> ${repRID}.${ref}.alignSampleData.log
+ samtools sort -@ `nproc` -O BAM -o ${ref}.sampled.sorted.bam ${ref}.sampled.bam
# index the sorted bam using Samtools
- echo "LOG: indexing sorted bam file" >> ${repRID}.${ref}.alignSampleData.err
- samtools index -@ `nproc` -b ${ref}.sampled.sorted.bam ${ref}.sampled.sorted.bam.bai 1>> ${repRID}.${ref}.alignSampleData.out 2>> ${repRID}.${ref}.alignSampleData.err;
+ echo "LOG: indexing sorted bam file" >> ${repRID}.${ref}.alignSampleData.log
+ samtools index -@ `nproc` -b ${ref}.sampled.sorted.bam ${ref}.sampled.sorted.bam.bai
"""
}
@@ -435,7 +421,6 @@ alignSampleQC.into {
process inferMetadata {
tag "${repRID}"
- publishDir "${logsDir}", mode: 'copy', pattern: "${repRID}.inferMetadata.{out,err}"
input:
path script_inferMeta
@@ -447,12 +432,11 @@ process inferMetadata {
output:
path "infer.csv" into inferMetadata
path "${repRID}.infer_experiment.txt" into inferExperiment
- path "${repRID}.inferMetadata.{out,err}" optional true
script:
"""
- hostname > ${repRID}.inferMetadata.err
- ulimit -a >> ${repRID}.inferMetadata.err
+ hostname > ${repRID}.inferMetadata.log
+ ulimit -a >> ${repRID}.inferMetadata.log
# collect alignment rates (round down to integers)
align_ercc=\$(echo \$(grep "Overall alignment rate" ERCC.alignSampleSummary.txt | cut -f2 -d ':' | cut -f2 -d ' ' | tr -d '%'))
@@ -469,7 +453,7 @@ process inferMetadata {
else
spike="no"
fi
- echo -e "LOG: Inference of strandedness results is: \${spike}" >> ${repRID}.inferMetadata.err
+ echo -e "LOG: Inference of strandedness results is: \${spike}" >> ${repRID}.inferMetadata.log
# determine species
if [ 1 -eq \$(echo \$(expr \${align_hu} ">=" 25)) ] && [ 1 -eq \$(echo \$(expr \${align_mo} "<" 25)) ]
@@ -483,28 +467,28 @@ process inferMetadata {
bam="GRCm.sampled.sorted.bam"
bed="./GRCm/bed/genome.bed"
else
- echo -e "LOG: ERROR - Inference of species returns an ambiguous result: hu=\${align_hu} mo=\${align_mo}" >> ${repRID}.inferMetadata.err
+ echo -e "LOG: ERROR - Inference of species returns an ambiguous result: hu=\${align_hu} mo=\${align_mo}" >> ${repRID}.inferMetadata.log
exit 1
fi
- echo -e "LOG: Inference of species results in: \${species}" >> ${repRID}.inferMetadata.err
+ echo -e "LOG: Inference of species results in: \${species}" >> ${repRID}.inferMetadata.log
# infer experimental setting from dedup bam
- echo "LOG: infer experimental setting from dedup bam" >> ${repRID}.inferMetadata.err
- infer_experiment.py -r "\${bed}" -i "\${bam}" 1>> ${repRID}.infer_experiment.txt 2>> ${repRID}.inferMetadata.err
+ echo "LOG: infer experimental setting from dedup bam" >> ${repRID}.inferMetadata.log
+ infer_experiment.py -r "\${bed}" -i "\${bam}" 1>> ${repRID}.infer_experiment.txt
- echo "LOG: determining endedness and strandedness from file" >> ${repRID}.inferMetadata.err
- ended=`bash inferMeta.sh endness ${repRID}.infer_experiment.txt` 1>> ${repRID}.inferMetadata.out 2>> ${repRID}.inferMetadata.err
- fail=`bash inferMeta.sh fail ${repRID}.infer_experiment.txt` 1>> ${repRID}.inferMetadata.out 2>> ${repRID}.inferMetadata.err
+ echo "LOG: determining endedness and strandedness from file" >> ${repRID}.inferMetadata.log
+ ended=`bash inferMeta.sh endness ${repRID}.infer_experiment.txt`
+ fail=`bash inferMeta.sh fail ${repRID}.infer_experiment.txt`
if [ \${ended} == "PairEnd" ]
then
ends="pe"
- percentF=`bash inferMeta.sh pef ${repRID}.infer_experiment.txt` 1>> ${repRID}.inferMetadata.out 2>> ${repRID}.inferMetadata.err
- percentR=`bash inferMeta.sh per ${repRID}.infer_experiment.txt` 1>> ${repRID}.inferMetadata.out 2>> ${repRID}.inferMetadata.err
+ percentF=`bash inferMeta.sh pef ${repRID}.infer_experiment.txt`
+ percentR=`bash inferMeta.sh per ${repRID}.infer_experiment.txt`
elif [ \${ended} == "SingleEnd" ]
then
ends="se"
- percentF=`bash inferMeta.sh sef ${repRID}.infer_experiment.txt` 1>> ${repRID}.inferMetadata.out 2>> ${repRID}.inferMetadata.err
- percentR=`bash inferMeta.sh ser ${repRID}.infer_experiment.txt` 1>> ${repRID}.inferMetadata.out 2>> ${repRID}.inferMetadata.err
+ percentF=`bash inferMeta.sh sef ${repRID}.infer_experiment.txt`
+ percentR=`bash inferMeta.sh ser ${repRID}.infer_experiment.txt`
fi
if [ 1 -eq \$(echo \$(expr \${percentF#*.} ">" 2500)) ] && [ 1 -eq \$(echo \$(expr \${percentR#*.} "<" 2500)) ]
then
@@ -516,10 +500,10 @@ process inferMetadata {
else
stranded="unstranded"
fi
- echo -e "LOG: stradedness set to \${stranded}" >> ${repRID}.inferMetadata.err
+ echo -e "LOG: stradedness set to \${stranded}" >> ${repRID}.inferMetadata.log
# write infered metadata to file
- echo "\${ends},\${stranded},\${spike},\${species},\${align_ercc},\${align_hu},\${align_mo},\${percentF},\${percentR},\${fail}" 1>> infer.csv 2>> ${repRID}.inferMetadata.err
+ echo "\${ends},\${stranded},\${spike},\${species},\${align_ercc},\${align_hu},\${align_mo},\${percentF},\${percentR},\${fail}" 1>> infer.csv
"""
}
@@ -573,7 +557,6 @@ speciesInfer.into {
*/
process getRef {
tag "${species}"
- publishDir "${logsDir}", mode: "copy", pattern: "${repRID}.getRef.{out,err}"
input:
val spike from spikeInfer_getRef
@@ -581,12 +564,11 @@ process getRef {
output:
tuple path ("hisat2", type: 'dir'), path ("bed", type: 'dir'), path ("*.fna"), path ("*.gtf") into reference
- path ("${repRID}.getRef.{out,err}")
script:
"""
- hostname > ${repRID}.getRef.err
- ulimit -a >> ${repRID}.getRef.err
+ hostname > ${repRID}.getRef.log
+ ulimit -a >> ${repRID}.getRef.log
export https_proxy=\${http_proxy}
# set the reference name
@@ -597,7 +579,7 @@ process getRef {
then
references=\$(echo ${referenceBase}/GRCh${refHuVersion})
else
- echo -e "LOG: ERROR - References could not be set!\nSpecies reference found: ${species}" >> ${repRID}.getRef.err
+ echo -e "LOG: ERROR - References could not be set!\nSpecies reference found: ${species}" >> ${repRID}.getRef.log
exit 1
fi
if [ "${spike}" == "yes" ]
@@ -607,23 +589,23 @@ process getRef {
then
reference=\$(echo \${references}/)
fi
- echo "LOG: species set to \${references}" >> ${repRID}.getRef.err
+ echo "LOG: species set to \${references}" >> ${repRID}.getRef.log
# retreive appropriate reference appropriate location
if [ ${referenceBase} == "s3://bicf-references" ]
then
- echo "LOG: grabbing reference files from S3" >> ${repRID}.getRef.err
- aws s3 cp "\${references}" /hisat2 ./ --recursive 1>> ${repRID}.getRef.out 2>> ${repRID}.getRef.err
- aws s3 cp "\${references}" /bed ./ --recursive 1>> ${repRID}.getRef.out 2>> ${repRID}.getRef.err
- aws s3 cp "\${references}" /*.fna --recursive 1>> ${repRID}.getRef.out 2>> ${repRID}.getRef.err
- aws s3 cp "\${references}" /*.gtf --recursive 1>> ${repRID}.getRef.out 2>> ${repRID}.getRef.err
+ echo "LOG: grabbing reference files from S3" >> ${repRID}.getRef.log
+ aws s3 cp "\${references}" /hisat2 ./ --recursive
+ aws s3 cp "\${references}" /bed ./ --recursive
+ aws s3 cp "\${references}" /*.fna --recursive
+ aws s3 cp "\${references}" /*.gtf --recursive
elif [ ${referenceBase} == "/project/BICF/BICF_Core/shared/gudmap/references" ]
then
- echo "LOG: using pre-defined locations for reference files" >> ${repRID}.getRef.err
- ln -s "\${references}"/hisat2 1>> ${repRID}.getRef.out 2>> ${repRID}.getRef.err
- ln -s "\${references}"/bed 1>> ${repRID}.getRef.out 2>> ${repRID}.getRef.err
- ln -s "\${references}"/genome.fna 1>> ${repRID}.getRef.out 2>> ${repRID}.getRef.err
- ln -s "\${references}"/genome.gtf 1>> ${repRID}.getRef.out 2>> ${repRID}.getRef.err
+ echo "LOG: using pre-defined locations for reference files" >> ${repRID}.getRef.log
+ ln -s "\${references}"/hisat2
+ ln -s "\${references}"/bed
+ ln -s "\${references}"/genome.fna
+ ln -s "\${references}"/genome.gtf
fi
"""
}
@@ -640,7 +622,6 @@ reference.into {
*/
process alignData {
tag "${repRID}"
- publishDir "${logsDir}", mode: "copy", pattern: "${repRID}.align.{out,err}"
input:
val ends from endsInfer_alignData
@@ -651,12 +632,11 @@ process alignData {
output:
tuple path ("${repRID}.sorted.bam"), path ("${repRID}.sorted.bam.bai") into rawBam
path ("*.alignSummary.txt") into alignQC
- path ("${repRID}.align.{out,err}")
script:
"""
- hostname > ${repRID}.align.err
- ulimit -a >> ${repRID}.align.err
+ hostname > ${repRID}.align.log
+ ulimit -a >> ${repRID}.align.log
# set stranded param for hisat2
if [ "${stranded}"=="unstranded" ]
@@ -679,25 +659,25 @@ process alignData {
# align the reads with Hisat 2
if [ "${ends}" == "se" ]
then
- echo "LOG: running Hisat2 with single-end settings" >> ${repRID}.align.err
- hisat2 -p `nproc` --add-chrname --un-gz ${repRID}.unal.gz -S ${repRID}.sam -x hisat2/genome \${strandedParam} -U ${fastq[0]} --summary-file ${repRID}.alignSummary.txt --new-summary 1>> ${repRID}.align.out 2>> ${repRID}.align.err
+ echo "LOG: running Hisat2 with single-end settings" >> ${repRID}.align.log
+ hisat2 -p `nproc` --add-chrname --un-gz ${repRID}.unal.gz -S ${repRID}.sam -x hisat2/genome \${strandedParam} -U ${fastq[0]} --summary-file ${repRID}.alignSummary.txt --new-summary
elif [ "${ends}" == "pe" ]
then
- echo "LOG: running Hisat2 with paired-end settings" >> ${repRID}.align.err
- hisat2 -p `nproc` --add-chrname --un-gz ${repRID}.unal.gz -S ${repRID}.sam -x hisat2/genome \${strandedParam} --no-mixed --no-discordant -1 ${fastq[0]} -2 ${fastq[1]} --summary-file ${repRID}.alignSummary.txt --new-summary 1>> ${repRID}.align.out 2>> ${repRID}.align.err
+ echo "LOG: running Hisat2 with paired-end settings" >> ${repRID}.align.log
+ hisat2 -p `nproc` --add-chrname --un-gz ${repRID}.unal.gz -S ${repRID}.sam -x hisat2/genome \${strandedParam} --no-mixed --no-discordant -1 ${fastq[0]} -2 ${fastq[1]} --summary-file ${repRID}.alignSummary.txt --new-summary
fi
# convert the output sam file to a sorted bam file using Samtools
- echo "LOG: converting from sam to bam" >> ${repRID}.align.err
- samtools view -1 -@ `nproc` -F 4 -F 8 -F 256 -o ${repRID}.bam ${repRID}.sam 1>> ${repRID}.align.out 2>> ${repRID}.align.err;
+ echo "LOG: converting from sam to bam" >> ${repRID}.align.log
+ samtools view -1 -@ `nproc` -F 4 -F 8 -F 256 -o ${repRID}.bam ${repRID}.sam
# sort the bam file using Samtools
- echo "LOG: sorting the bam file" >> ${repRID}.align.err
- samtools sort -@ `nproc` -O BAM -o ${repRID}.sorted.bam ${repRID}.bam 1>> ${repRID}.align.out 2>> ${repRID}.align.err;
+ echo "LOG: sorting the bam file" >> ${repRID}.align.log
+ samtools sort -@ `nproc` -O BAM -o ${repRID}.sorted.bam ${repRID}.bam
# index the sorted bam using Samtools
- echo "LOG: indexing sorted bam file" >> ${repRID}.align.err
- samtools index -@ `nproc` -b ${repRID}.sorted.bam ${repRID}.sorted.bam.bai 1>> ${repRID}.align.out 2>> ${repRID}.align.err;
+ echo "LOG: indexing sorted bam file" >> ${repRID}.align.log
+ samtools index -@ `nproc` -b ${repRID}.sorted.bam ${repRID}.sorted.bam.bai
"""
}
@@ -712,7 +692,6 @@ rawBam.into {
process dedupData {
tag "${repRID}"
publishDir "${outDir}/bam", mode: 'copy', pattern: "*.deduped.bam"
- publishDir "${logsDir}", mode: 'copy', pattern: "${repRID}.dedup.{out,err}"
input:
tuple path (bam), path (bai) from rawBam_dedupData
@@ -721,28 +700,27 @@ process dedupData {
tuple path ("${repRID}.sorted.deduped.bam"), path ("${repRID}.sorted.deduped.bam.bai") into dedupBam
tuple path ("${repRID}.sorted.deduped.*.bam"), path ("${repRID}.sorted.deduped.*.bam.bai") into dedupChrBam
path ("*.deduped.Metrics.txt") into dedupQC
- path ("${repRID}.dedup.{out,err}")
script:
"""
- hostname > ${repRID}.dedup.err
- ulimit -a >> ${repRID}.dedup.err
+ hostname > ${repRID}.dedup.log
+ ulimit -a >> ${repRID}.dedup.log
# remove duplicated reads using Picard's MarkDuplicates
- echo "LOG: running picard MarkDuplicates to remove duplicate reads" >> ${repRID}.dedup.err
- java -jar /picard/build/libs/picard.jar MarkDuplicates I=${bam} O=${repRID}.deduped.bam M=${repRID}.deduped.Metrics.txt REMOVE_DUPLICATES=true 1>> ${repRID}.dedup.out 2>> ${repRID}.dedup.err
+ echo "LOG: running picard MarkDuplicates to remove duplicate reads" >> ${repRID}.dedup.log
+ java -jar /picard/build/libs/picard.jar MarkDuplicates I=${bam} O=${repRID}.deduped.bam M=${repRID}.deduped.Metrics.txt REMOVE_DUPLICATES=true
# sort the bam file using Samtools
- samtools sort -@ `nproc` -O BAM -o ${repRID}.sorted.deduped.bam ${repRID}.deduped.bam 1>>${repRID}.dedup.out 2>> ${repRID}.dedup.err
+ samtools sort -@ `nproc` -O BAM -o ${repRID}.sorted.deduped.bam ${repRID}.deduped.bam
# index the sorted bam using Samtools
- samtools index -@ `nproc` -b ${repRID}.sorted.deduped.bam ${repRID}.sorted.deduped.bam.bai 1>>${repRID}.dedup.out 2>> ${repRID}.dedup.err
+ samtools index -@ `nproc` -b ${repRID}.sorted.deduped.bam ${repRID}.sorted.deduped.bam.bai
# split the deduped BAM file for multi-threaded tin calculation
for i in `samtools view ${repRID}.sorted.deduped.bam | cut -f3 | sort | uniq`;
do
- echo "echo \"LOG: splitting each chromosome into its own BAM and BAI files with Samtools\" >> ${repRID}.dedup.err; samtools view -b ${repRID}.sorted.deduped.bam \${i} > ${repRID}.sorted.deduped.\${i}.bam; samtools index -@ `nproc` -b ${repRID}.sorted.deduped.\${i}.bam ${repRID}.sorted.deduped.\${i}.bam.bai"
- done | parallel -j `nproc` -k 1>>${repRID}.dedup.out 2>> ${repRID}.dedup.err
+ echo "echo \"LOG: splitting each chromosome into its own BAM and BAI files with Samtools\"; samtools view -b ${repRID}.sorted.deduped.bam \${i} 1>> ${repRID}.sorted.deduped.\${i}.bam; samtools index -@ `nproc` -b ${repRID}.sorted.deduped.\${i}.bam ${repRID}.sorted.deduped.\${i}.bam.bai"
+ done | parallel -j `nproc` -k
"""
}
@@ -758,7 +736,6 @@ dedupBam.into {
*/
process makeBigWig {
tag "${repRID}"
- publishDir "${logsDir}", mode: 'copy', pattern: "${repRID}.makeBigWig.{out,err}"
publishDir "${outDir}/bigwig", mode: 'copy', pattern: "${repRID}.bw"
input:
@@ -766,16 +743,15 @@ process makeBigWig {
output:
path ("${repRID}.bw")
- path ("${repRID}.makeBigWig.{out,err}")
script:
"""
- hostname > ${repRID}.makeBigWig.err
- ulimit -a >> ${repRID}.makeBigWig.err
+ hostname > ${repRID}.makeBigWig.log
+ ulimit -a >> ${repRID}.makeBigWig.log
# run bamCoverage
- echo "LOG: Running bigWig bamCoverage" >> ${repRID}.makeBigWig.err
- bamCoverage -p `nproc` -b ${bam} -o ${repRID}.bw 1>> ${repRID}.makeBigWig.out 2>> ${repRID}.makeBigWig.err
+ echo "LOG: Running bigWig bamCoverage" >> ${repRID}.makeBigWig.log
+ bamCoverage -p `nproc` -b ${bam} -o ${repRID}.bw
"""
}
@@ -785,7 +761,6 @@ process makeBigWig {
process countData {
tag "${repRID}"
publishDir "${outDir}/countData", mode: 'copy', pattern: "${repRID}*.countTable.csv"
- publishDir "${logsDir}", mode: 'copy', pattern: "${repRID}.countData.{out,err}"
input:
path script_calculateTPM
@@ -797,42 +772,41 @@ process countData {
output:
path ("*.countTable.csv") into counts
path ("*.countData.summary") into countsQC
- path ("${repRID}.countData.{out,err}")
script:
"""
- hostname > ${repRID}.countData.err
- ulimit -a >> ${repRID}.countData.err
+ hostname > ${repRID}.countData.log
+ ulimit -a >> ${repRID}.countData.log
# determine strandedness and setup strandig for countData
stranding=0;
if [ "${stranded}" == "unstranded" ]
then
stranding=0
- echo "LOG: strandedness set to unstranded [0]" >> ${repRID}.countData.err
+ echo "LOG: strandedness set to unstranded [0]" >> ${repRID}.countData.log
elif [ "${stranded}" == "forward" ]
then
stranding=1
- echo "LOG: strandedness set to forward stranded [1]" >> ${repRID}.countData.err
+ echo "LOG: strandedness set to forward stranded [1]" >> ${repRID}.countData.log
elif [ "${stranded}" == "reverse" ]
then
stranding=2
- echo "LOG: strandedness set to forward stranded [2]" >> ${repRID}.countData.err
+ echo "LOG: strandedness set to forward stranded [2]" >> ${repRID}.countData.log
fi
# run featureCounts
- echo "LOG: running featureCounts on the data" >> ${repRID}.countData.err
+ echo "LOG: running featureCounts on the data" >> ${repRID}.countData.log
if [ "${ends}" == "se" ]
then
- featureCounts -T `nproc` -a ./genome.gtf -G ./genome.fna -g 'gene_name' -o ${repRID}.countData -s \${stranding} -R SAM --primary --ignoreDup ${repRID}.sorted.deduped.bam 1>> ${repRID}.countData.out 2>> ${repRID}.countData.err
+ featureCounts -T `nproc` -a ./genome.gtf -G ./genome.fna -g 'gene_name' -o ${repRID}.countData -s \${stranding} -R SAM --primary --ignoreDup ${repRID}.sorted.deduped.bam
elif [ "${ends}" == "pe" ]
then
- featureCounts -T `nproc` -a ./genome.gtf -G ./genome.fna -g 'gene_name' -o ${repRID}.countData -s \${stranding} -p -B -R SAM --primary --ignoreDup ${repRID}.sorted.deduped.bam 1>> ${repRID}.countData.out 2>> ${repRID}.countData.err
+ featureCounts -T `nproc` -a ./genome.gtf -G ./genome.fna -g 'gene_name' -o ${repRID}.countData -s \${stranding} -p -B -R SAM --primary --ignoreDup ${repRID}.sorted.deduped.bam
fi
# calculate TPM from the resulting countData table
- echo "LOG: calculating TPM with R" >> ${repRID}.countData.err
- Rscript calculateTPM.R --count "${repRID}.countData" 1>> ${repRID}.countData.out 2>> ${repRID}.countData.err
+ echo "LOG: calculating TPM with R" >> ${repRID}.countData.log
+ Rscript calculateTPM.R --count "${repRID}.countData"
"""
}
@@ -841,23 +815,21 @@ process countData {
*/
process fastqc {
tag "${repRID}"
- publishDir "${logsDir}", mode: 'copy', pattern: "${repRID}.fastqc.{out,err}"
input:
path (fastq) from fastqs_fastqc
output:
path ("*_fastqc.zip") into fastqc
- path ("${repRID}.fastqc.{out,err}")
script:
"""
- hostname > ${repRID}.fastqc.err
- ulimit -a >> ${repRID}.fastqc.err
+ hostname > ${repRID}.fastqc.log
+ ulimit -a >> ${repRID}.fastqc.log
# run fastqc
- echo "LOG: beginning FastQC analysis of the data" >> ${repRID}.fastqc.err
- fastqc *.fastq.gz -o . 1>> ${repRID}.fastqc.out 2>> ${repRID}.fastqc.err
+ echo "LOG: beginning FastQC analysis of the data" >> ${repRID}.fastqc.log
+ fastqc *.fastq.gz -o .
"""
}
@@ -866,7 +838,6 @@ process fastqc {
*/
process dataQC {
tag "${repRID}"
- publishDir "${logsDir}", mode: 'copy', pattern: "${repRID}.dataQC.{out,err}"
input:
path script_tinHist
@@ -878,18 +849,16 @@ process dataQC {
output:
path "${repRID}.tin.hist.tsv" into tin
path "${repRID}.insertSize.inner_distance_freq.txt" into innerDistance
- path "${repRID}.dataQC.{out,err}"
-
script:
"""
- hostname > ${repRID}.dataQC.err
- ulimit -a >> ${repRID}.dataQC.err
+ hostname > ${repRID}.dataQC.log
+ ulimit -a >> ${repRID}.dataQC.log
# calcualte TIN values per feature on each chromosome
echo -e "geneID\tchrom\ttx_start\ttx_end\tTIN" > ${repRID}.sorted.deduped.tin.xls
for i in `cat ./bed/genome.bed | cut -f1 | sort | uniq`; do
- echo "echo \"LOG: running tin.py on \${i}\" >> ${repRID}.dataQC.err; tin.py -i ${repRID}.sorted.deduped.\${i}.bam -r ./bed/genome.bed 1>>${repRID}.dataQC.log 2>>${repRID}.dataQC.err; cat ${repRID}.sorted.deduped.\${i}.tin.xls | tr -s \"\\w\" \"\\t\" | grep -P \\\"\\\\t\${i}\\\\t\\\";";
- done | parallel -j `nproc` -k 1>> ${repRID}.sorted.deduped.tin.xls 2>>${repRID}.dataQC.err
+ echo "echo \"LOG: running tin.py on \${i}\" >> ${repRID}.dataQC.log; tin.py -i ${repRID}.sorted.deduped.\${i}.bam -r ./bed/genome.bed; cat ${repRID}.sorted.deduped.\${i}.tin.xls | tr -s \"\\w\" \"\\t\" | grep -P \\\"\\\\t\${i}\\\\t\\\";";
+ done | parallel -j `nproc` -k 1>> ${repRID}.sorted.deduped.tin.xls
# bin TIN values
python3 ${script_tinHist} -r ${repRID}
@@ -897,7 +866,7 @@ process dataQC {
# calculate inner-distances for PE data
if [ "${ends}" == "pe" ]
then
- inner_distance.py -i "${bam}" -o ${repRID}.insertSize -r ./bed/genome.bed 1>>${repRID}.dataQC.out 2>>${repRID}.dataQC.err
+ inner_distance.py -i "${bam}" -o ${repRID}.insertSize -r ./bed/genome.bed
else
touch ${repRID}.insertSize.inner_distance_freq.txt
fi
@@ -909,7 +878,6 @@ process dataQC {
*/
process aggrQC {
tag "${repRID}"
- publishDir "${logsDir}", mode: 'copy', pattern: "${repRID}.aggrQC.{out,err}"
input:
path multiqcConfig
@@ -935,12 +903,11 @@ process aggrQC {
val studyRID
output:
- path "${repRID}.aggrQC.{out,err}" optional true
script:
"""
- hostname > ${repRID}.aggrQC.err
- ulimit -a >> ${repRID}.aggrQC.err
+ hostname > ${repRID}.aggrQC.log
+ ulimit -a >> ${repRID}.aggrQC.log
# make RID table
echo -e "Replicate RID\tExperiment RID\tStudy RID" > rid.tsv