From 84dd8e501b7f91f0f791ce141cb684bdd1b8ff6e Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 1 Mar 2021 22:38:38 -0600
Subject: [PATCH] Put multiple when's into a single line
---
rna-seq.nf | 152 +++++++++--------------------------------------------
1 file changed, 24 insertions(+), 128 deletions(-)
diff --git a/rna-seq.nf b/rna-seq.nf
index e733020..186a895 100644
--- a/rna-seq.nf
+++ b/rna-seq.nf
@@ -599,8 +599,7 @@ process fastqc {
path "fastqFileError.csv" into fastqFileError_fl
when:
- fastqCountError == 'false'
- fastqReadError == 'false'
+ fastqCountError == "false" && fastqReadError == "false"
script:
"""
@@ -688,8 +687,7 @@ process seqwho {
path "inferError.csv" into inferError_fl
when:
- fastqCountError == "false"
- fastqReadError == "false"
+ fastqCountError == "false" && fastqReadError == "false"
script:
"""
@@ -1019,8 +1017,7 @@ process getRefERCC {
tuple path ("hisat2", type: 'dir'), path ("*.fna"), path ("*.gtf") into refERCC
when:
- fastqCountError == "false"
- fastqReadError == "false"
+ fastqCountError == "false" && fastqReadError == "false"
script:
"""
@@ -1083,16 +1080,13 @@ process trimData {
path ("readLength.csv") into readLengthInfer_fl
when:
- fastqCountError == "false"
- fastqReadError == "false"
- fastqFileError == "false"
- seqtypeError == "false"
- speciesErrorSeqwho == "false"
+ fastqCountError == "false" && fastqReadError == "false" && fastqFileError == "false" && seqtypeError == "false" && speciesErrorSeqwho == "false"
script:
"""
hostname > ${repRID}.trimData.log
ulimit -a >> ${repRID}.trimData.log
+ echo fastqFileError ${fastqFileError}
# trim fastq's using trim_galore and extract median read length
echo -e "LOG: trimming ${ends}" >> ${repRID}.trimData.log
@@ -1147,11 +1141,7 @@ process downsampleData {
path ("sampled.{1,2}.fq") into fastqsSample
when:
- fastqCountError == "false"
- fastqReadError == "false"
- fastqFileError == "false"
- seqtypeError == "false"
- speciesErrorSeqwho == "false"
+ fastqCountError == "false" && fastqReadError == "false" && fastqFileError == "false" && seqtypeError == "false" && speciesErrorSeqwho == "false"
script:
"""
@@ -1202,10 +1192,7 @@ process alignSampleDataERCC {
path ("ERCC.alignSampleSummary.txt") into alignSampleQC_ERCC
when:
- fastqCountError == "false"
- fastqReadError == "false"
- fastqFileError == "false"
- seqtypeError == "false"
+ fastqCountError == "false" && fastqReadError == "false" && fastqFileError == "false" && seqtypeError == "false"
script:
"""
@@ -1300,12 +1287,7 @@ process getRef {
tuple path ("hisat2", type: 'dir'), path ("*.bed"), path ("*.fna"), path ("*.gtf"), path ("geneID.tsv"), path ("Entrez.tsv") into reference
when:
- fastqCountError == "false"
- fastqReadError == "false"
- fastqFileError == "false"
- seqtypeError == "false"
- speciesErrorSeqwho == "false"
- speciesError == "false"
+ fastqCountError == "false" && fastqReadError == "false" && fastqFileError == "false" && seqtypeError == "false" && speciesErrorSeqwho == "false" && speciesError == "false"
script:
"""
@@ -1412,12 +1394,7 @@ process alignSampleData {
path ("*.alignSampleSummary.txt") into alignSampleQC
when:
- fastqCountError == "false"
- fastqReadError == "false"
- fastqFileError == "false"
- seqtypeError == "false"
- speciesErrorSeqwho == "false"
- speciesError == "false"
+ fastqCountError == "false" && fastqReadError == "false" && fastqFileError == "false" && seqtypeError == "false" && speciesErrorSeqwho == "false" && speciesError == "false"
script:
"""
@@ -1478,12 +1455,7 @@ process inferMetadata {
path "${repRID}.infer_experiment.txt" into inferExperiment
when:
- fastqCountError == "false"
- fastqReadError == "false"
- fastqFileError == "false"
- seqtypeError == "false"
- speciesErrorSeqwho == "false"
- speciesError == "false"
+ fastqCountError == "false" && fastqReadError == "false" && fastqFileError == "false" && seqtypeError == "false" && speciesErrorSeqwho == "false" && speciesError == "false"
script:
"""
@@ -1589,12 +1561,7 @@ process checkMetadata {
path ("outputBagRID.csv") optional true into outputBagRID_fl_dummy
when:
- fastqCountError == "false"
- fastqReadError == "false"
- fastqFileError == "false"
- seqtypeError == "false"
- speciesErrorSeqwho == "false"
- speciesError == "false"
+ fastqCountError == "false" && fastqReadError == "false" && fastqFileError == "false" && seqtypeError == "false" && speciesErrorSeqwho == "false" && speciesError == "false"
script:
"""
@@ -1726,12 +1693,7 @@ process alignData {
path ("*.alignSummary.txt") into alignQC
when:
- fastqCountError == "false"
- fastqReadError == "false"
- fastqFileError == "false"
- seqtypeError == "false"
- speciesErrorSeqwho == "false"
- speciesError == "false"
+ fastqCountError == "false" && fastqReadError == "false" && fastqFileError == "false" && seqtypeError == "false" && speciesErrorSeqwho == "false" && speciesError == "false"
script:
"""
@@ -1807,13 +1769,7 @@ process dedupData {
path ("*.deduped.Metrics.txt") into dedupQC
when:
- fastqCountError == "false"
- fastqReadError == "false"
- fastqFileError == "false"
- seqtypeError == "false"
- speciesErrorSeqwho == "false"
- speciesError == "false"
- pipelineError == "false"
+ fastqCountError == "false" && fastqReadError == "false" && fastqFileError == "false" && seqtypeError == "false" && speciesErrorSeqwho == "false" && speciesError == "false" && pipelineError == "false"
script:
"""
@@ -1870,13 +1826,7 @@ process makeBigWig {
path ("${repRID}_sorted.deduped.bw") into bigwig
when:
- fastqCountError == "false"
- fastqReadError == "false"
- fastqFileError == "false"
- seqtypeError == "false"
- speciesErrorSeqwho == "false"
- speciesError == "false"
- pipelineError == "false"
+ fastqCountError == "false" && fastqReadError == "false" && fastqFileError == "false" && seqtypeError == "false" && speciesErrorSeqwho == "false" && speciesError == "false" && pipelineError == "false"
script:
"""
@@ -1918,13 +1868,7 @@ process countData {
path ("assignedReads.csv") into assignedReadsInfer_fl
when:
- fastqCountError == "false"
- fastqReadError == "false"
- fastqFileError == "false"
- seqtypeError == "false"
- speciesErrorSeqwho == "false"
- speciesError == "false"
- pipelineError == "false"
+ fastqCountError == "false" && fastqReadError == "false" && fastqFileError == "false" && seqtypeError == "false" && speciesErrorSeqwho == "false" && speciesError == "false" && pipelineError == "false"
script:
"""
@@ -2007,13 +1951,7 @@ process dataQC {
path "${repRID}_insertSize.inner_distance_freq.txt" into innerDistance
when:
- fastqCountError == "false"
- fastqReadError == "false"
- fastqFileError == "false"
- seqtypeError == "false"
- speciesErrorSeqwho == "false"
- speciesError == "false"
- pipelineError == "false"
+ fastqCountError == "false" && fastqReadError == "false" && fastqFileError == "false" && seqtypeError == "false" && speciesErrorSeqwho == "false" && speciesError == "false" && pipelineError == "false"
script:
"""
@@ -2107,13 +2045,7 @@ process aggrQC {
path "${repRID}.multiqc_data.json" into multiqcJSON
when:
- fastqCountError == "false"
- fastqReadError == "false"
- fastqFileError == "false"
- seqtypeError == "false"
- speciesErrorSeqwho == "false"
- speciesError == "false"
- pipelineError == "false"
+ fastqCountError == "false" && fastqReadError == "false" && fastqFileError == "false" && seqtypeError == "false" && speciesErrorSeqwho == "false" && speciesError == "false" && pipelineError == "false"
script:
"""
@@ -2306,14 +2238,7 @@ process uploadExecutionRun {
path ("executionRunRID.csv") into executionRunRID_fl
when:
- upload
- fastqCountError == "false"
- fastqReadError == "false"
- fastqFileError == "false"
- seqtypeError == "false"
- speciesErrorSeqwho == "false"
- speciesError == "false"
- pipelineError == "false"
+ upload && fastqCountError == "false" && fastqReadError == "false" && fastqFileError == "false" && seqtypeError == "false" && speciesErrorSeqwho == "false" && speciesError == "false" && pipelineError == "false"
script:
"""
@@ -2423,14 +2348,7 @@ process uploadQC {
path ("qcRID.csv") into qcRID_fl
when:
- upload
- fastqCountError == "false"
- fastqReadError == "false"
- fastqFileError == "false"
- seqtypeError == "false"
- speciesErrorSeqwho == "false"
- speciesError == "false"
- pipelineError == "false"
+ upload && fastqCountError == "false" && fastqReadError == "false" && fastqFileError == "false" && seqtypeError == "false" && speciesErrorSeqwho == "false" && speciesError == "false" && pipelineError == "false"
script:
"""
@@ -2505,14 +2423,7 @@ process uploadProcessedFile {
path ("${repRID}_Output_Bag.zip") into outputBag
when:
- upload
- fastqCountError == "false"
- fastqReadError == "false"
- fastqFileError == "false"
- seqtypeError == "false"
- speciesErrorSeqwho == "false"
- speciesError == "false"
- pipelineError == "false"
+ upload && fastqCountError == "false" && fastqReadError == "false" && fastqFileError == "false" && seqtypeError == "false" && speciesErrorSeqwho == "false" && speciesError == "false" && pipelineError == "false"
script:
"""
@@ -2610,14 +2521,7 @@ process uploadOutputBag {
path ("outputBagRID.csv") into outputBagRID_fl
when:
- upload
- fastqCountError == "false"
- fastqReadError == "false"
- fastqFileError == "false"
- seqtypeError == "false"
- speciesErrorSeqwho == "false"
- speciesError == "false"
- pipelineError == "false"
+ upload && fastqCountError == "false" && fastqReadError == "false" && fastqFileError == "false" && seqtypeError == "false" && speciesErrorSeqwho == "false" && speciesError == "false" && pipelineError == "false"
script:
"""
@@ -2696,13 +2600,7 @@ process finalizeExecutionRun {
when:
upload
- fastqCountError == "false"
- fastqReadError == "false"
- fastqFileError == "false"
- seqtypeError == "false"
- speciesErrorSeqwho == "false"
- speciesError == "false"
- pipelineError == "false"
+ fastqCountError == "false" && fastqReadError == "false" && fastqFileError == "false" && seqtypeError == "false" && speciesErrorSeqwho == "false" && speciesError == "false" && pipelineError == "false"
script:
"""
@@ -2759,8 +2657,7 @@ process failPreExecutionRun {
path ("executionRunRID.csv") into executionRunRID_preFail_fl
when:
- upload
- fastqCountError == "true" || fastqReadError == "true" || fastqFileError == "true" || seqtypeError == "true" || speciesError == "true"
+ upload && fastqCountError == "true" || fastqReadError == "true" || fastqFileError == "true" || seqtypeError == "true" || speciesError == "true"
script:
"""
@@ -2875,8 +2772,7 @@ process failExecutionRun {
val pipelineError_species
when:
- upload
- pipelineError == 'true'
+ upload && pipelineError == 'true'
script:
"""
--
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