From 7728d8fcc55e0766653144ee3efbfb46ef100f18 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 4 Jan 2021 21:55:49 -0600
Subject: [PATCH] Try double [ on if or
---
workflow/rna-seq.nf | 40 ++++++++++++++++++++--------------------
1 file changed, 20 insertions(+), 20 deletions(-)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 97f9462..9235c3b 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -505,7 +505,7 @@ readLengthInfer_fl.splitCsv(sep: ",", header: false).separate(
readLengthInfer
)
-// Replicate infered read length for multiple process inputs
+// Replicate inferred read length for multiple process inputs
readLengthInfer.into {
readLengthInfer_aggrQC
readLengthInfer_uploadQC
@@ -761,7 +761,7 @@ process inferMetadata {
# infer experimental setting from dedup bam
echo -e "LOG: infer experimental setting from dedup bam" >> ${repRID}.inferMetadata.log
infer_experiment.py -r "\${bed}" -i "\${bam}" 1>> ${repRID}.infer_experiment.txt
- echo -e "LOG: infered" >> ${repRID}.inferMetadata.log
+ echo -e "LOG: inferred" >> ${repRID}.inferMetadata.log
ended=`bash ${script_inferMeta} endness ${repRID}.infer_experiment.txt`
fail=`bash ${script_inferMeta} fail ${repRID}.infer_experiment.txt`
@@ -789,7 +789,7 @@ process inferMetadata {
fi
echo -e "LOG: stradedness set to: \${stranded}" >> ${repRID}.inferMetadata.log
- # write infered metadata to file
+ # write inferred metadata to file
echo "\${ends},\${stranded},\${spike},\${species},\${align_ercc},\${align_hu},\${align_mo},\${percentF},\${percentR},\${fail}" 1>> infer.csv
"""
}
@@ -853,7 +853,7 @@ speciesInfer.into {
}
/*
- * checkMetadata: checks the submitted metada against infered
+ * checkMetadata: checks the submitted metada against inferred
*/
process checkMetadata {
tag "${repRID}"
@@ -878,15 +878,15 @@ process checkMetadata {
ulimit -a >> ${repRID}.checkMetadata.log
pipelineError=false
- # check if submitted metadata matches infered
+ # check if submitted metadata matches inferred
if [ "${endsMeta}" != "${endsInfer}" ]
then
pipelineError=true
pipelineError_ends=true
- echo -e "LOG: ends do not match: Submitted=${endsMeta}; Infered=${endsInfer}" >> ${repRID}.checkMetadata.log
+ echo -e "LOG: ends do not match: Submitted=${endsMeta}; Inferred=${endsInfer}" >> ${repRID}.checkMetadata.log
else
pipelineError_ends=false
- echo -e "LOG: ends matches: Submitted=${endsMeta}; Infered=${endsInfer}" >> ${repRID}.checkMetadata.log
+ echo -e "LOG: ends matches: Submitted=${endsMeta}; Inferred=${endsInfer}" >> ${repRID}.checkMetadata.log
fi
if [ "${strandedMeta}" != "${strandedInfer}" ]
then
@@ -894,39 +894,39 @@ process checkMetadata {
pipelineError_stranded=true
if [ "${strandedMeta}" == "stranded" ]
then
- if [ "${strandedInfer}" == "forward"] | [ "${strandedInfer}" == "reverse" ]
+ if [[ "${strandedInfer}" == "forward" ]] || [[ "${strandedInfer}" == "reverse" ]]
then
pipelineError=false
pipelineError_stranded=false
- echo -e "LOG: stranded matches: Submitted=${strandedMeta}; Infered=${strandedInfer}" >> ${repRID}.checkMetadata.log
+ echo -e "LOG: stranded matches: Submitted=${strandedMeta}; Inferred=${strandedInfer}" >> ${repRID}.checkMetadata.log
else
- echo -e "LOG: stranded does not match: Submitted=${strandedMeta}; Infered=${strandedInfer}" >> ${repRID}.checkMetadata.log
+ echo -e "LOG: stranded does not match: Submitted=${strandedMeta}; Inferred=${strandedInfer}" >> ${repRID}.checkMetadata.log
fi
else
- echo -e "LOG: stranded does not match: Submitted=${strandedMeta}; Infered=${strandedInfer}" >> ${repRID}.checkMetadata.log
+ echo -e "LOG: stranded does not match: Submitted=${strandedMeta}; Inferred=${strandedInfer}" >> ${repRID}.checkMetadata.log
fi
else
pipelineError=false
pipelineError_stranded=false
- echo -e "LOG: stranded matches: Submitted=${strandedMeta}; Infered=${strandedInfer}" >> ${repRID}.checkMetadata.log
+ echo -e "LOG: stranded matches: Submitted=${strandedMeta}; Inferred=${strandedInfer}" >> ${repRID}.checkMetadata.log
fi
if [ "${spikeMeta}" != "${spikeInfer}" ]
then
pipelineError=true
pipelineError_spike=true
- echo -e "LOG: spike does not match: Submitted=${spikeMeta}; Infered=${spikeInfer}" >> ${repRID}.checkMetadata.log
+ echo -e "LOG: spike does not match: Submitted=${spikeMeta}; Inferred=${spikeInfer}" >> ${repRID}.checkMetadata.log
else
pipelineError_spike=false
- echo -e "LOG: stranded matches: Submitted=${spikeMeta}; Infered=${spikeInfer}" >> ${repRID}.checkMetadata.log
+ echo -e "LOG: stranded matches: Submitted=${spikeMeta}; Inferred=${spikeInfer}" >> ${repRID}.checkMetadata.log
fi
if [ "${speciesMeta}" != "${speciesInfer}" ]
then
pipelineError=true
pipelineError_species=true
- echo -e "LOG: species does not match: Submitted=${speciesMeta}; Infered=${speciesInfer}" >> ${repRID}.checkMetadata.log
+ echo -e "LOG: species does not match: Submitted=${speciesMeta}; Inferred=${speciesInfer}" >> ${repRID}.checkMetadata.log
else
pipelineError_species=false
- echo -e "LOG: species matches: Submitted=${speciesMeta}; Infered=${speciesInfer}" >> ${repRID}.checkMetadata.log
+ echo -e "LOG: species matches: Submitted=${speciesMeta}; Inferred=${speciesInfer}" >> ${repRID}.checkMetadata.log
fi
# create dummy output bag rid if failure
@@ -1454,7 +1454,7 @@ assignedReadsInfer_fl.splitCsv(sep: ",", header: false).separate(
assignedReadsInfer
)
-// Replicate infered assigned reads for multiple process inputs
+// Replicate inferred assigned reads for multiple process inputs
assignedReadsInfer.into {
assignedReadsInfer_aggrQC
assignedReadsInfer_uploadQC
@@ -1499,7 +1499,7 @@ rawReadsInfer_fl.splitCsv(sep: ",", header: false).separate(
rawReadsInfer
)
-// Replicate infered raw reads for multiple process inputs
+// Replicate inferred raw reads for multiple process inputs
rawReadsInfer.into {
rawReadsInfer_aggrQC
rawReadsInfer_uploadQC
@@ -1654,9 +1654,9 @@ process aggrQC {
echo -e "Submitter\t${speciesM}\t${endsM}\t${strandedM}\t${spikeM}\t-\t-\t'${readLengthM}'\t-" >> metadata.tsv
if [ "${params.speciesForce}" == "" ]
then
- echo -e "Infered\t${speciesI}\t${endsI}\t${strandedI}\t${spikeI}\t-\t-\t-\t-" >> metadata.tsv
+ echo -e "Inferred\t${speciesI}\t${endsI}\t${strandedI}\t${spikeI}\t-\t-\t-\t-" >> metadata.tsv
else
- echo -e "Infered\t${speciesI} (FORCED)\t${endsI}\t${strandedI}\t${spikeI}\t-\t-\t-\t-" >> metadata.tsv
+ echo -e "Inferred\t${speciesI} (FORCED)\t${endsI}\t${strandedI}\t${spikeI}\t-\t-\t-\t-" >> metadata.tsv
fi
echo -e "Measured\t-\t${endsManual}\t-\t-\t'${rawReadsI}'\t'${assignedReadsI}'\t'${readLengthI}'\t'${tinMedI}'" >> metadata.tsv
--
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