diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 0c56150ca6923ba7cea1c6da0699e92b83f2f1e6..eaeff79747ff0e111fbfccd07b2506b7b57842d6 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -46,7 +46,7 @@ script_inferMeta = Channel.fromPath("${baseDir}/scripts/inferMeta.sh")
*/
process getBag {
tag "${repRID}"
- publishDir "${logsDir}", mode: "copy", pattern: "*.getBag.err"
+ publishDir "${logsDir}", mode: "copy", pattern: "${repRID}.getBag.{out,err}"
input:
path credential, stageAs: "credential.json" from deriva
@@ -58,16 +58,17 @@ process getBag {
script:
"""
- hostname >>${repRID}.getBag.err
- ulimit -a >>${repRID}.getBag.err
+ hostname > ${repRID}.getBag.err
+ ulimit -a >> ${repRID}.getBag.err
export https_proxy=\${http_proxy}
# link credential file for authentication
- ln -sf `readlink -e credential.json` ~/.deriva/credential.json 2>>${repRID}.getBag.err
- echo "LOG: deriva credentials linked" >>${repRID}.getBag.err
+ 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
# deriva-download replicate RID
- deriva-download-cli dev.gudmap.org --catalog 2 ${derivaConfig} . rid=${repRID} 2>>${repRID}.getBag.err
+ 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>> ${repRID}.getBag.err
"""
}
@@ -76,7 +77,7 @@ process getBag {
*/
process getData {
tag "${repRID}"
- publishDir "${logsDir}", mode: "copy", pattern: "*.getData.err"
+ publishDir "${logsDir}", mode: "copy", pattern: "${repRID}.getData.{out,err}"
input:
path script_bdbagFetch
@@ -88,29 +89,29 @@ process getData {
path ("**/File.csv") into fileMeta
path ("**/Experiment Settings.csv") into experimentSettingsMeta
path ("**/Experiment.csv") into experimentMeta
- path ("${repRID}.getData.err")
+ path ("${repRID}.getData.{out,err}")
script:
"""
- hostname >>${repRID}.getData.err
- ulimit -a >>${repRID}.getData.err
+ hostname > ${repRID}.getData.err
+ ulimit -a >> ${repRID}.getData.err
export https_proxy=\${http_proxy}
# link deriva cookie for authentication
- ln -sf `readlink -e deriva-cookies.txt` ~/.bdbag/deriva-cookies.txt >>${repRID}.getData.err
- echo "LOG: deriva cookie linked" >>${repRID}.getData.err
+ ln -sf `readlink -e deriva-cookies.txt` ~/.bdbag/deriva-cookies.txt 1>> ${repRID}.getData.out 2>> ${repRID}.getData.err
+ echo "LOG: deriva cookie linked" >> ${repRID}.getData.err
# get bagit basename
- replicate=\$(basename "${bagit}" | cut -d "." -f1)
- echo "LOG: \${replicate}" >>${repRID}.getData.err
+ replicate=\$(basename "${bagit}" | cut -d "." -f1) 1>> ${repRID}.getData.out 2>> ${repRID}.getData.err
+ echo "LOG: \${replicate}" >> ${repRID}.getData.err
# unzip bagit
- unzip ${bagit} 2>>${repRID}.getData.err
- echo "LOG: replicate bdbag unzipped" >>${repRID}.getData.err
+ unzip ${bagit} 2>> ${repRID}.getData.err 1>> ${repRID}.getData.out 2>> ${repRID}.getData.err
+ echo "LOG: replicate bdbag unzipped" >> ${repRID}.getData.err
# bagit fetch fastq"s only and rename by repRID
- sh ${script_bdbagFetch} \${replicate} ${repRID} 2>>${repRID}.getData.err
- echo "LOG: replicate bdbag fetched" >>${repRID}.getData.err
+ sh ${script_bdbagFetch} \${replicate} ${repRID} 1>> ${repRID}.getData.out 2>> ${repRID}.getData.err
+ echo "LOG: replicate bdbag fetched" >> ${repRID}.getData.err
"""
}
@@ -125,7 +126,7 @@ fastqs.into {
*/
process parseMetadata {
tag "${repRID}"
- publishDir "${logsDir}", mode: "copy", pattern: "*.parseMetadata.err"
+ publishDir "${logsDir}", mode: "copy", pattern: "${repRID}.parseMetadata.{out,err}"
input:
path script_parseMeta
@@ -136,35 +137,36 @@ process parseMetadata {
output:
path "design.csv" into metadata
+ path "${repRID}.parseMetadata.{out,err}"
script:
"""
- hostname >>${repRID}.parseMetadata.err
- ulimit -a >>${repRID}.parseMetadata.err
+ hostname > ${repRID}.parseMetadata.err
+ ulimit -a >> ${repRID}.parseMetadata.err
# 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.err
# 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.err
# Manually 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.err
# Get strandedness metadata
stranded=\$(python3 ${script_parseMeta} -r ${repRID} -m "${experimentSettingsMeta}" -p stranded -e \${endsManual})
- echo "LOG: strandedness metadata parsed: \${stranded}" >>${repRID}.parseMetadata.err
+ echo "LOG: strandedness metadata parsed: \${stranded}" >> ${repRID}.parseMetadata.err
# 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.err
# 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}" >> ${repRID}.parseMetadata.err
# Save design file
echo "\${rep},\${endsMeta},\${endsManual},\${stranded},\${spike},\${species}" > design.csv
@@ -194,6 +196,7 @@ endsManual.into {
}
stranded.into {
stranded_alignData
+ stranded_featureCounts
}
spike.into{
spike_getRef
@@ -207,19 +210,20 @@ species.into {
*/
process getRef {
tag "${species_getRef}"
- publishDir "${logsDir}", mode: "copy", pattern: "*.getRef.err"
+ publishDir "${logsDir}", mode: "copy", pattern: "${repRID}.getRef.{out,err}"
input:
val spike_getRef
val species_getRef
output:
- path ("*") into reference
-
+ tuple path ("hisat2", type: 'dir'), path ("bed", type: 'dir'), path ("*.fna"), path ("*.gtf") into reference
+ path ("${repRID}.getRef.{out,err}")
+
script:
"""
- hostname >>${repRID}.getRef.err
- ulimit -a >>${repRID}.getRef.err
+ hostname > ${repRID}.getRef.err
+ ulimit -a >> ${repRID}.getRef.err
export https_proxy=\${http_proxy}
# run set the reference name
@@ -230,6 +234,7 @@ process getRef {
then
references=\$(echo ${referenceBase}/GRCh${refHuVersion})
else
+ echo -e "LOG: ERROR - References could not be set!\nSpecies reference found: ${species_getRef}" >> ${repRID}.getRef.err
exit 1
fi
if [ "${spike_getRef}" == "yes" ]
@@ -239,20 +244,23 @@ process getRef {
then
reference=\$(echo \${references}/)
fi
+ echo "LOG: species set to \${references}" >> ${repRID}.getRef.err
# retreive appropriate reference appropriate location
if [ ${referenceBase} == "s3://bicf-references" ]
then
- aws s3 cp "\${references}" /hisat2 ./ --recursive >>${repRID}.getRef.err
- aws s3 cp "\${references}" /bed ./ --recursive >>${repRID}.getRef.err
- aws s3 cp "\${references}" /*.fna --recursive >>${repRID}.getRef.err
- aws s3 cp "\${references}" /*.gtf --recursive >>${repRID}.getRef.err
+ 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
elif [ ${referenceBase} == "/project/BICF/BICF_Core/shared/gudmap/references" ]
then
- ln -s "\${references}"/hisat2 >>${repRID}.getRef.err
- ln -s "\${references}"/bed >>${repRID}.getRef.err
- ln -s "\${references}"/genome.fna >>${repRID}.getRef.err
- ln -s "\${references}"/genome.gtf >>${repRID}.getRef.err
+ 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>> ${repRID}.getRef.err
fi
"""
}
@@ -269,7 +277,7 @@ reference.into {
*/
process trimData {
tag "${repRID}"
- publishDir "${logsDir}", mode: "copy", pattern: "*.trimData.*"
+ publishDir "${logsDir}", mode: "copy", pattern: "${repRID}.trimData.{out,err}"
input:
val endsManual_trimData
@@ -278,21 +286,22 @@ process trimData {
output:
path ("*.fq.gz") into fastqs_trimmed
path ("*_trimming_report.txt") into trimQC
- path ("${repRID}.trimData.log")
- path ("${repRID}.trimData.err")
+ path ("${repRID}.trimData.{out,err}")
script:
"""
- hostname >>${repRID}.trimData.err
- ulimit -a >>${repRID}.trimData.err
+ hostname > ${repRID}.trimData.err
+ ulimit -a >> ${repRID}.trimData.err
- # trim fastqs
+ #Trim fastqs using trim_galore
if [ "${endsManual_trimData}" == "se" ]
then
- trim_galore --gzip -q 25 --illumina --length 35 --basename ${repRID} -j `nproc` ${fastq[0]} 1>>${repRID}.trimData.log 2>>${repRID}.trimData.err
+ 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>> ${repRID}.trimData.err
elif [ "${endsManual_trimData}" == "pe" ]
then
- trim_galore --gzip -q 25 --illumina --length 35 --paired --basename ${repRID} -j `nproc` ${fastq[0]} ${fastq[1]} 1>>${repRID}.trimData.log 2>>${repRID}.trimData.err
+ 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>> ${repRID}.trimData.err
fi
"""
}
@@ -302,7 +311,7 @@ process trimData {
*/
process alignData {
tag "${repRID}"
- publishDir "${logsDir}", mode: "copy", pattern: "*.align.{out,err}"
+ publishDir "${logsDir}", mode: "copy", pattern: "${repRID}.align.{out,err}"
input:
val endsManual_alignData
@@ -313,27 +322,35 @@ process alignData {
output:
tuple val ("${repRID}"), path ("${repRID}.sorted.bam"), path ("${repRID}.sorted.bam.bai") into rawBam
path ("*.alignSummary.txt") into alignQC
- path ("${repRID}.align.out")
- path ("${repRID}.align.err")
+ path ("${repRID}.align.{out,err}")
script:
"""
- hostname >${repRID}.align.err
- ulimit -a >>${repRID}.align.err
+ hostname > ${repRID}.align.err
+ ulimit -a >> ${repRID}.align.err
- # align reads
+ #Align the reads with Hisat 2
if [ "${endsManual_alignData}" == "se" ]
then
- hisat2 -p `nproc` --add-chrname --un-gz ${repRID}.unal.gz -S ${repRID}.sam -x hisat2/genome ${stranded_alignData} -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.err
+ hisat2 -p `nproc` --add-chrname --un-gz ${repRID}.unal.gz -S ${repRID}.sam -x hisat2/genome ${stranded_alignData} -U ${fastq[0]} --summary-file ${repRID}.alignSummary.txt --new-summary 1>> ${repRID}.align.out 2>> ${repRID}.align.err
elif [ "${endsManual_alignData}" == "pe" ]
then
- hisat2 -p `nproc` --add-chrname --un-gz ${repRID}.unal.gz -S ${repRID}.sam -x hisat2/genome ${stranded_alignData} --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.err
+ hisat2 -p `nproc` --add-chrname --un-gz ${repRID}.unal.gz -S ${repRID}.sam -x hisat2/genome ${stranded_alignData} --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
fi
- # convert sam to bam and sort and index
- samtools view -1 -@ `nproc` -F 4 -F 8 -F 256 -o ${repRID}.bam ${repRID}.sam 1>>${repRID}.align.out 2>>${repRID}.align.err;
- samtools sort -@ `nproc` -O BAM -o ${repRID}.sorted.bam ${repRID}.bam 1>>${repRID}.align.out 2>>${repRID}.align.err;
- samtools index -@ `nproc` -b ${repRID}.sorted.bam ${repRID}.sorted.bam.bai 1>>${repRID}.align.out 2>>${repRID}.align.err;
+ #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;
+
+ #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;
+
+ #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>> ${repRID}.align.err;
"""
}
@@ -348,26 +365,32 @@ rawBam.into {
process dedupData {
tag "${repRID}"
publishDir "${outDir}/bam", mode: 'copy', pattern: "*.deduped.bam"
- publishDir "${logsDir}", mode: 'copy', pattern: "*.dedup.{out,err}"
+ publishDir "${logsDir}", mode: 'copy', pattern: "${repRID}.dedup.{out,err}"
input:
set val (repRID), path (inBam), path (inBai) from rawBam_dedupData
output:
- tuple val ("${repRID}"), path ("${repRID}.sorted.deduped.bam"), path ("${repRID}.sorted.deduped.bam.bai") into dedupBam
+ tuple path ("${repRID}.sorted.deduped.bam"), path ("${repRID}.sorted.deduped.bam.bai") into dedupBam
path ("*.deduped.Metrics.txt") into dedupQC
- path ("${repRID}.dedup.out")
- path ("${repRID}.dedup.err")
+ path ("${repRID}.dedup.{out,err}")
script:
"""
- hostname >${repRID}.dedup.err
- ulimit -a >>${repRID}.dedup.err
+ hostname > ${repRID}.dedup.err
+ ulimit -a >> ${repRID}.dedup.err
+
+ # remove duplicated reads using Picard's MarkDuplicates
+ echo "LOG: running picard MarkDuplicates to remove duplicate reads" >> ${repRID}.dedup.err
+ java -jar /picard/build/libs/picard.jar MarkDuplicates I=${inBam} O=${repRID}.deduped.bam M=${repRID}.deduped.Metrics.txt REMOVE_DUPLICATES=true 1>> ${repRID}.dedup.out 2>> ${repRID}.dedup.err
- # remove duplicated reads
- java -jar /picard/build/libs/picard.jar MarkDuplicates I=${inBam} O=${repRID}.deduped.bam M=${repRID}.deduped.Metrics.txt REMOVE_DUPLICATES=true 1>>${repRID}.dedup.out 2>> ${repRID}.dedup.err
- samtools sort -@ `nproc` -O BAM -o ${repRID}.sorted.deduped.bam ${repRID}.deduped.bam 1>>${repRID}.dedup.out 2>> ${repRID}.dedup.err
- samtools index -@ `nproc` -b ${repRID}.sorted.deduped.bam ${repRID}.sorted.deduped.bam.bai 1>>${repRID}.dedup.out 2>> ${repRID}.dedup.err
+ #Use SamTools to sort the now deduped bam file
+ echo "LOG: sorting the deduped bam file" >> ${repRID}.dedup.err
+ samtools sort -@ `nproc` -O BAM -o ${repRID}.sorted.deduped.bam ${repRID}.deduped.bam 1>> ${repRID}.dedup.out 2>> ${repRID}.dedup.err
+
+ #Use SamTools to index the now sorted deduped bam file
+ echo "LOG: indexing the sorted deduped bam file" >> ${repRID}.dedup.err
+ samtools index -@ `nproc` -b ${repRID}.sorted.deduped.bam ${repRID}.sorted.deduped.bam.bai 1>> ${repRID}.dedup.out 2>> ${repRID}.dedup.err
"""
}
@@ -383,17 +406,24 @@ dedupBam.into {
*/
process makeBigWig {
tag "${repRID}"
- publishDir "${logsDir}", mode: 'copy', pattern: "*.makeBigWig.err"
+ publishDir "${logsDir}", mode: 'copy', pattern: "${repRID}.makeBigWig.{out,err}"
+ publishDir "${outDir}/bigwig", mode: 'copy', pattern: "${repRID}.bw"
input:
- set val (repRID), path (inBam), path (inBai) from dedupBam_makeBigWig
+ set path (inBam), path (inBai) from dedupBam_makeBigWig
output:
path ("${repRID}.bw")
+ path ("${repRID}.makeBigWig.{out,err}")
script:
"""
- bamCoverage -p `nproc` -b ${inBam} -o ${repRID}.bw
+ hostname > ${repRID}.makeBigWig.err
+ ulimit -a >> ${repRID}.makeBigWig.err
+
+ #Run bamCoverage
+ echo "LOG: Running bigWig bamCoverage" >> ${repRID}.makeBigWig.err
+ bamCoverage -p `nproc` -b ${inBam} -o ${repRID}.bw 1>> ${repRID}.makeBigWig.out 2>> ${repRID}.makeBigWig.err
"""
}
@@ -407,24 +437,43 @@ process makeFeatureCounts {
input:
path script_calculateTPM
- tuple val (repRID), path (bam), path (bai) from dedupBam_makeFeatureCounts
+ tuple path (bam), path (bai) from dedupBam_makeFeatureCounts
path reference_makeFeatureCounts
val endsManual_featureCounts
output:
path ("*.countTable.csv") into counts
path ("*.featureCounts.summary") into countsQC
+ path ("${repRID}.makeFeatureCounts.{out,err}")
script:
"""
+ hostname > ${repRID}.makeFeatureCounts.err
+ ulimit -a >> ${repRID}.makeFeatureCounts.err
+
+ #Determine strandedness and setup strandig for featureCounts
+ stranding=0;
+ if [ "${stranded_featureCounts}" == "--rna-strandness F" ] || [ "${stranded_featureCounts}" == "--rna-strandness FR" ]
+ then
+ stranding=1
+ echo "LOG: strandedness set to stranded [1]" >> ${repRID}.makeFeatureCounts.err
+ else
+ stranding=0
+ echo "LOG: strandedness set to unstranded [0]" >> ${repRID}.makeFeatureCounts.err
+ fi;
+ #Run featureCounts
+ echo "LOG: running featureCounts on the data" >> ${repRID}.makeFeatureCounts.err
if [ "${endsManual_featureCounts }" == "se" ]
then
- featureCounts -R SAM -p -G ./genome.fna -T `nproc` -s 1 -a ./genome.gtf -o ${repRID}.featureCounts -g 'gene_name' ${repRID}.sorted.deduped.bam;
+ featureCounts -R SAM -p -G ./genome.fna -T `nproc` -s \${stranding} -a ./genome.gtf -o ${repRID}.featureCounts -g 'gene_name' --primary --ignoreDup ${repRID}.sorted.deduped.bam 1>> ${repRID}.makeFeatureCounts.out 2>> ${repRID}.makeFeatureCounts.err
elif [ "${endsManual_featureCounts }" == "pe" ]
then
- featureCounts -R SAM -p -G ./genmome.fna -T `nproc` -s 1 -p -a ./genome.gtf -o ${repRID}.featureCounts -g 'gene_name' ${repRID}.sorted.deduped.bam;
+ featureCounts -R SAM -p -G ./genmome.fna -T `nproc` -s \${stranding} -p -a ./genome.gtf -o ${repRID}.featureCounts -g 'gene_name' --primary --ignoreDup -B ${repRID}.sorted.deduped.bam 1>> ${repRID}.makeFeatureCounts.out 2>> ${repRID}.makeFeatureCounts.err
fi
- Rscript calculateTPM.R --count "${repRID}.featureCounts";
+
+ #Calculate TMP from the resulting featureCounts table
+ echo "LOG: calculating TMP with R" >> ${repRID}.makeFeatureCounts.err
+ Rscript calculateTPM.R --count "${repRID}.featureCounts" 1>> ${repRID}.makeFeatureCounts.out 2>> ${repRID}.makeFeatureCounts.err
"""
}
@@ -434,21 +483,23 @@ process makeFeatureCounts {
process fastqc {
tag "${repRID}"
publishDir "${outDir}/fastqc", mode: 'copy', pattern: "*_fastqc.zip"
- publishDir "${logsDir}", mode: 'copy', pattern: "*.fastq.err"
+ 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.err
+ ulimit -a >> ${repRID}.fastqc.err
# run fastqc
- fastqc *.fastq.gz -o . >>${repRID}.fastqc.err
+ echo "LOG: beginning FastQC analysis of the data" >> ${repRID}.fastqc.err
+ fastqc *.fastq.gz -o . 1>> ${repRID}.fastqc.out 2>> ${repRID}.fastqc.err
"""
}
@@ -458,38 +509,40 @@ process fastqc {
process inferMetadata {
tag "${repRID}"
- publishDir "${logsDir}", mode: 'copy', pattern: "*.rseqc.err"
+ publishDir "${logsDir}", mode: 'copy', pattern: "${repRID}.rseqc.{out,err}"
input:
path script_inferMeta
path reference_inferMeta
- set val (repRID), path (inBam), path (inBai) from dedupBam_inferMeta
+ set path (inBam), path (inBai) from dedupBam_inferMeta
output:
path "infer.csv" into inferedMetadata
path "${inBam.baseName}.tin.xls" into tin
path "${repRID}.insertSize.inner_distance_freq.txt" optional true into innerDistance
-
+ path "${repRID}.rseqc.{out,err}" optional true
script:
"""
- hostname >${repRID}.rseqc.err
- ulimit -a >>${repRID}.rseqc.err
+ hostname > ${repRID}.rseqc.err
+ ulimit -a >> ${repRID}.rseqc.err
# infer experimental setting from dedup bam
- infer_experiment.py -r ./bed/genome.bed -i "${inBam}" >${repRID}.rseqc.log
+ echo "LOG: running inference from bed file" >> ${repRID}.rseqc.err
+ infer_experiment.py -r ./bed/genome.bed -i "${inBam}" > ${repRID}.rseqc.log 2>> ${repRID}.rseqc.err
- endness=`bash inferMeta.sh endness ${repRID}.rseqc.log`
- fail=`bash inferMeta.sh fail ${repRID}.rseqc.log`
+ echo "LOG: determining endedness and strandedness from file" >> ${repRID}.rseqc.err
+ endness=`bash inferMeta.sh endness ${repRID}.rseqc.log` 1>> ${repRID}.rseqc.out 2>> ${repRID}.rseqc.err
+ fail=`bash inferMeta.sh fail ${repRID}.rseqc.log` 1>> ${repRID}.rseqc.out 2>> ${repRID}.rseqc.err
if [ \${endness} == "PairEnd" ]
then
- percentF=`bash inferMeta.sh pef ${repRID}.rseqc.log`
- percentR=`bash inferMeta.sh per ${repRID}.rseqc.log`
- inner_distance.py -i "${inBam}" -o ${repRID}.insertSize -r ./bed/genome.bed
+ percentF=`bash inferMeta.sh pef ${repRID}.rseqc.log` 1>> ${repRID}.rseqc.out 2>> ${repRID}.rseqc.err
+ percentR=`bash inferMeta.sh per ${repRID}.rseqc.log` 1>> ${repRID}.rseqc.out 2>> ${repRID}.rseqc.err
+ inner_distance.py -i "${inBam}" -o ${repRID}.insertSize -r ./bed/genome.bed 1>> ${repRID}.rseqc.out 2>> ${repRID}.rseqc.err
elif [ \${endness} == "SingleEnd" ]
then
- percentF=`bash inferMeta.sh sef ${repRID}.rseqc.log`
- percentR=`bash inferMeta.sh ser ${repRID}.rseqc.log`
+ percentF=`bash inferMeta.sh sef ${repRID}.rseqc.log` 1>> ${repRID}.rseqc.out 2>> ${repRID}.rseqc.err
+ percentR=`bash inferMeta.sh ser ${repRID}.rseqc.log` 1>> ${repRID}.rseqc.out 2>> ${repRID}.rseqc.err
fi
if [ \$percentF -gt 0.25 ] && [ \$percentR -lt 0.25 ]
then
@@ -513,11 +566,12 @@ process inferMetadata {
stranded="unstranded"
strategy="us"
fi
+ echo -e "LOG: strategy set to \${strategy}\nStranded set to ${stranded}" >> ${repRID}.rseqc.err
# calcualte TIN values per feature
- tin.py -i "${inBam}" -r ./bed/genome.bed
+ tin.py -i "${inBam}" -r ./bed/genome.bed 1>> ${repRID}.rseqc.out 2>> ${repRID}.rseqc.err
# write infered metadata to file
- echo \${endness},\${stranded},\${strategy},\${percentF},\${percentR},\${fail} > infer.csv
+ echo \${endness},\${stranded},\${strategy},\${percentF},\${percentR},\${fail} > infer.csv 2>> ${repRID}.rseqc.err
"""
-}
\ No newline at end of file
+}