diff --git a/CHANGELOG.md b/CHANGELOG.md
index c90e24a68ed21255944f7cdcccba3377c9bfc91a..94f20980b833a1803b5120c0dfd8fb04bc83201d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,6 +7,7 @@
* Add seqwho
* Add seqwho results to multiqc report
* Modify repository structure to allow for use with XPACK-DNANEXUS
+* Add override for endness
**Background**
* Add memory limit (75%) per thread for samtools sort (#108)
diff --git a/README.md b/README.md
index 04f49d7d7d3ebe739023ccfa30a099136e48b19d..33fb73d09c9dc8668f61a71c5029940fbc690404 100644
--- a/README.md
+++ b/README.md
@@ -56,12 +56,14 @@ To Run:
* `--inputBagForce` utilizes a local replicate inputBag instead of downloading from the data-hub (still requires accurate repRID input)
* eg: `--inputBagForce test_data/bag/Q-Y5F6_inputBag_xxxxxxxx.zip` (must be the expected bag structure, this example will not work because it is a test bag)
* `--fastqsForce` utilizes local fastq's instead of downloading from the data-hub (still requires accurate repRID input)
- * eg: `--fastqsForce 'test_data/fastq/small/Q-Y5F6_1M.R{1,2}.fastq.gz'` (note the quotes around fastq's which must me named in the correct standard [*\*.R1.fastq.gz and/or \*.R2.fastq.gz*] and in the correct order)
+ * eg: `--fastqsForce 'test_data/fastq/small/Q-Y5F6_1M.R{1,2}.fastq.gz'` (note the quotes around fastq's which must me named in the correct standard [*\*.R1.fastq.gz and/or \*.R2.fastq.gz*] and in the correct order, also consider using `endsForce` if the endness doesn't match submitted value)
* `--speciesForce` forces the species to be "Mus musculus" or "Homo sapiens", it bypasses a metadata mismatch or an ambiguous species error
* eg: `--speciesForce 'Mus musculus'`
+ * `--endsForce` forces the endness to be "se", or "pe", it bypasses a metadata mismatch error
+ * eg: `--endsForce 'pe'`
* `--strandedForce` forces the strandedness to be "forward", "reverse" or "unstranded", it bypasses a metadata mismatch error
* eg: `--strandedForce 'unstranded'`
- * `--spikeForce` forces the spike-in to be "false" or "true", it bypasses a metadata mismatch error
+ * `--spikeForce` forces the spike-in to be "false", or "true", it bypasses a metadata mismatch error
* eg: `--spikeForce 'true'`
* Tracking parameters ([Tracking Site](http://bicf.pipeline.tracker.s3-website-us-east-1.amazonaws.com/)):
* `--ci` boolean (default = false)
diff --git a/rna-seq.nf b/rna-seq.nf
index f7619777cd7104c4e5ab954ded7c8521fa72f387..78d24fa22be5b1cdacf2cb89884df7e56113cf00 100644
--- a/rna-seq.nf
+++ b/rna-seq.nf
@@ -26,6 +26,7 @@ params.track = false
params.refSource = "biohpc"
params.inputBagForce = ""
params.fastqsForce = ""
+params.endsForce = ""
params.speciesForce = ""
params.strandedForce = ""
params.spikeForce = ""
@@ -64,6 +65,7 @@ logsDir = "${outDir}/Logs"
upload = params.upload
inputBagForce = params.inputBagForce
fastqsForce = params.fastqsForce
+endsForce = params.endsForce
speciesForce = params.speciesForce
strandedForce = params.strandedForce
spikeForce = params.spikeForce
@@ -1469,6 +1471,7 @@ process inferMetadata {
path sampledBam
path reference_inferMetadata
path script_inferMeta
+ val endsForce
val strandedForce
val fastqCountError from fastqCountError_inferMetadata
val fastqReadError from fastqReadError_inferMetadata
@@ -1489,41 +1492,47 @@ process inferMetadata {
hostname > ${repRID}.inferMetadata.log
ulimit -a >> ${repRID}.inferMetadata.log
- # infer experimental setting from dedup bam
- echo -e "LOG: infer experimental setting from bam" >> ${repRID}.inferMetadata.log
- infer_experiment.py -r ./genome.bed -i ${sampledBam} 1>> ${repRID}.infer_experiment.txt
- echo -e "LOG: inferred" >> ${repRID}.inferMetadata.log
+ # infer experimental setting from dedup bam
+ echo -e "LOG: infer experimental setting from bam" >> ${repRID}.inferMetadata.log
+ infer_experiment.py -r ./genome.bed -i ${sampledBam} 1>> ${repRID}.infer_experiment.txt
+ 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`
- if [ \${ended} == "PairEnd" ]
- then
- ends="pe"
- percentF=`bash ${script_inferMeta} pef ${repRID}.infer_experiment.txt`
- percentR=`bash ${script_inferMeta} per ${repRID}.infer_experiment.txt`
- elif [ \${ended} == "SingleEnd" ]
- then
- ends="se"
- percentF=`bash ${script_inferMeta} sef ${repRID}.infer_experiment.txt`
- percentR=`bash ${script_inferMeta} ser ${repRID}.infer_experiment.txt`
- fi
- echo -e "LOG: percentage reads in the same direction as gene: \${percentF}" >> ${repRID}.inferMetadata.log
- echo -e "LOG: percentage reads in the opposite direction as gene: \${percentR}" >> ${repRID}.inferMetadata.log
- if [ 1 -eq \$(echo \$(expr \${percentF#*.} ">" 2500)) ] && [ 1 -eq \$(echo \$(expr \${percentR#*.} "<" 2500)) ]
- then
- stranded="forward"
- elif [ 1 -eq \$(echo \$(expr \${percentR#*.} ">" 2500)) ] && [ 1 -eq \$(echo \$(expr \${percentF#*.} "<" 2500)) ]
- then
- stranded="reverse"
- else
- stranded="unstranded"
- fi
- echo -e "LOG: stradedness set to: \${stranded}" >> ${repRID}.inferMetadata.log
- if [ "${strandedForce}" != "" ]
- then
- stranded=${strandedForce}
- echo -e "LOG: spike-in metadata forced: \${stranded}" >> ${repRID}.inferMetadata.log
- fi
+ ended=`bash ${script_inferMeta} endness ${repRID}.infer_experiment.txt`
+ fail=`bash ${script_inferMeta} fail ${repRID}.infer_experiment.txt`
+ if [ \${ended} == "PairEnd" ]
+ then
+ ends="pe"
+ percentF=`bash ${script_inferMeta} pef ${repRID}.infer_experiment.txt`
+ percentR=`bash ${script_inferMeta} per ${repRID}.infer_experiment.txt`
+ elif [ \${ended} == "SingleEnd" ]
+ then
+ ends="se"
+ percentF=`bash ${script_inferMeta} sef ${repRID}.infer_experiment.txt`
+ percentR=`bash ${script_inferMeta} ser ${repRID}.infer_experiment.txt`
+ fi
+ echo -e "LOG: percentage reads in the same direction as gene: \${percentF}" >> ${repRID}.inferMetadata.log
+ echo -e "LOG: percentage reads in the opposite direction as gene: \${percentR}" >> ${repRID}.inferMetadata.log
+ if [ 1 -eq \$(echo \$(expr \${percentF#*.} ">" 2500)) ] && [ 1 -eq \$(echo \$(expr \${percentR#*.} "<" 2500)) ]
+ then
+ stranded="forward"
+ elif [ 1 -eq \$(echo \$(expr \${percentR#*.} ">" 2500)) ] && [ 1 -eq \$(echo \$(expr \${percentF#*.} "<" 2500)) ]
+ then
+ stranded="reverse"
+ else
+ stranded="unstranded"
+ fi
+ echo -e "LOG: ends set to: \${ends}" >> ${repRID}.inferMetadata.log
+ if [ "${endsForce}" != "" ]
+ then
+ ends=${endsForce}
+ echo -e "LOG: ends metadata forced: \${ends}" >> ${repRID}.inferMetadata.log
+ fi
+ echo -e "LOG: stradedness set to: \${stranded}" >> ${repRID}.inferMetadata.log
+ if [ "${strandedForce}" != "" ]
+ then
+ stranded=${strandedForce}
+ echo -e "LOG: spike-in metadata forced: \${stranded}" >> ${repRID}.inferMetadata.log
+ fi
# write inferred metadata to file
echo "\${ends},\${stranded},\${percentF},\${percentR},\${fail}" > infer.csv
@@ -1632,9 +1641,16 @@ process checkMetadata {
fi
if [ "${endsMeta}" != "${endsInfer}" ]
then
- pipelineError=true
- pipelineError_ends=true
- echo -e "LOG: ends do not match: Submitted=${endsMeta}; Inferred=${endsInfer}" >> ${repRID}.checkMetadata.log
+ if [ "${params.endsForce}" != "" ]
+ then
+ pipelineError=false
+ pipelineError_ends=false
+ echo -e "LOG: ends forced: Submitted=${endsMeta}; Inferred=${endsInfer}" >> ${repRID}.checkMetadata.log
+ else
+ pipelineError=true
+ pipelineError_ends=true
+ echo -e "LOG: ends do not match: Submitted=${endsMeta}; Inferred=${endsInfer}" >> ${repRID}.checkMetadata.log
+ fi
else
pipelineError_ends=false
echo -e "LOG: ends matches: Submitted=${endsMeta}; Inferred=${endsInfer}" >> ${repRID}.checkMetadata.log