From 03e05d4c9786930656b1dff206d456b8be34c8f7 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Wed, 26 Aug 2020 12:56:17 -0500
Subject: [PATCH] Add species override
---
.gitlab-ci.yml | 14 ++++++++
CHANGELOG.md | 7 ++--
README.md | 2 ++
workflow/conf/multiqc_config.yaml | 2 ++
workflow/rna-seq.nf | 56 +++++++++++++++++++++++++++----
5 files changed, 72 insertions(+), 9 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 8f4c222..7aff1aa 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -201,6 +201,20 @@ override_fastq:
paths:
- fastqOverride_PE_multiqc_data.json
expire_in: 7 days
+
+override_species:
+ stage: integration
+ script:
+ - hostname
+ - ulimit -a
+ - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5ER --speciesForce 'Homo sapiens' --ci true
+ - find . -type f -name "multiqc_data.json" -exec cp {} ./speciesOverride_PE_multiqc_data.json \;
+ artifacts:
+ name: "$CI_JOB_NAME"
+ when: always
+ paths:
+ - speciesOverride_PE_multiqc_data.json
+ expire_in: 7 days
consistency:
stage: consistency
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 104cc84..3db82b0 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,12 +6,15 @@
* MultiQC output custom talbes (html+JSON):
* Run table: *Session ID* and *Pipeline Version*
* Reference Table: *Species*, *Genome Reference Consortium Build*, *Genome Reference Consortium Patch*, *GENCODE Annotation Release* (ouputs both human and mouse versions)
-* Add inputBag override param (`inputBagForce`)
+* Add inputBag override param (`inputBagForce`) [`*.zip`]
* Uses provided inputBag instead of downloading from data-hub
* Still requires matching repRID input param
* Add fastq override param (`fastqsForce`) [`R1`,`R2`]
* Uses provided fastq instead of downloading from data-hub
* Still requires matching repRID input param and will pull inputBag from data-hub to access submitted metadata for reporting
+* Add species override param (`speciesForce`) [`Mus musculus` or `Homo sapiens`]
+ * forces the use of the provided species
+ * ignors infered ambiguous species
**Background**
* Add GeneSymbol/EnsemblID/EntrezID translation files to references
@@ -19,7 +22,7 @@
*Known Bugs*
* outputBag does not contain fetch for processed data
* Does not include automatic data upload
-* Override params (inputBag and fastq) are't checked for integrity
+* Override params (inputBag, fastq, species) are't checked for integrity
<hr>
diff --git a/README.md b/README.md
index e96460d..49069c5 100644
--- a/README.md
+++ b/README.md
@@ -53,6 +53,8 @@ To Run:
* eg: `--inputBagForce test_data/bag/Replicate_Q-Y5F6.zip` (must be the expected bag structure)
* `--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)
+ * `--speciesForce` forces the species to be "Mus musculus" or "Homo sapiens", it bypasses ambiguous species error
+ * eg: `--speciesForce 'Mus musculus'`
* Tracking parameters ([Tracking Site](http://bicf.pipeline.tracker.s3-website-us-east-1.amazonaws.com/)):
* `--ci` boolean (default = false)
* `--dev` boolean (default = false)
diff --git a/workflow/conf/multiqc_config.yaml b/workflow/conf/multiqc_config.yaml
index e6e85c6..0c780d9 100644
--- a/workflow/conf/multiqc_config.yaml
+++ b/workflow/conf/multiqc_config.yaml
@@ -73,6 +73,7 @@ custom_data:
Session
Session ID
Pipeline Version
+ Input
rid:
file_format: 'tsv'
section_name: 'RID'
@@ -83,6 +84,7 @@ custom_data:
scale: false
format: '{}'
headers:
+ Replicate
Replicate RID
Experiment RID
Study RID
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 387e7f1..b6687df 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -22,6 +22,7 @@ params.outDir = "${baseDir}/../output"
// Define override input variable
params.inputBagForce = ""
params.fastqsForce = ""
+params.speciesForce = ""
// Parse input variables
deriva = Channel
@@ -38,7 +39,7 @@ outDir = params.outDir
logsDir = "${outDir}/Logs"
inputBagForce = params.inputBagForce
fastqsForce = params.fastqsForce
-
+speciesForce = params.speciesForce
// Define fixed files
derivaConfig = Channel.fromPath("${baseDir}/conf/replicate_export_config.json")
@@ -562,7 +563,24 @@ process inferMetadata {
bed="./GRCm/bed/genome.bed"
else
echo -e "LOG: ERROR - inference of species returns an ambiguous result: hu=\${align_hu} mo=\${align_mo}" >> ${repRID}.inferMetadata.log
- exit 1
+ if [ "${speciesForce}" == "" ]
+ then
+ exit 1
+ fi
+ fi
+ if [ "${speciesForce}" != "" ]
+ then
+ echo -e "LOG: species overridden to: ${speciesForce}"
+ species="${speciesForce}"
+ if [ "${speciesForce}" == "Homo sapiens" ]
+ then
+ bam="GRCh.sampled.sorted.bam"
+ bed="./GRCh/bed/genome.bed"
+ elif [ "${speciesForce}" == "Mus musculus" ]
+ then
+ bam="GRCm.sampled.sorted.bam"
+ bed="./GRCm/bed/genome.bed"
+ fi
fi
echo -e "LOG: inference of species results in: \${species}" >> ${repRID}.inferMetadata.log
@@ -1064,20 +1082,44 @@ process aggrQC {
ulimit -a >> ${repRID}.aggrQC.log
# make run table
+ if [ "${params.inputBagForce}" == "" ] && [ "${params.fastqsForce}" == "" ] && [ "${params.speciesForce}" == "" ]
+ then
+ input="default"
+ else
+ input="override:"
+ if [ "${params.inputBagForce}" != "" ]
+ then
+ input=\$(echo \${input} inputBag)
+ fi
+ if [ "${params.fastqsForce}" != "" ]
+ then
+ input=\$(echo \${input} fastq)
+ fi
+ if [ "${params.speciesForce}" != "" ]
+ then
+ input=\$(echo \${input} species)
+ fi
+ fi
echo -e "LOG: creating run table" >> ${repRID}.aggrQC.log
- echo -e "Session\tSession ID\tPipeline Version" > run.tsv
- echo -e "Session\t${workflow.sessionId}\t${workflow.manifest.version}" >> run.tsv
+ echo -e "Session\tSession ID\tPipeline Version\tInput" > run.tsv
+ echo -e "Session\t${workflow.sessionId}\t${workflow.manifest.version}\t\${input}" >> run.tsv
+
# make RID table
echo -e "LOG: creating RID table" >> ${repRID}.aggrQC.log
- echo -e "Replicate RID\tExperiment RID\tStudy RID" > rid.tsv
- echo -e "${repRID}\t${expRID}\t${studyRID}" >> rid.tsv
+ echo -e "Replicate\tReplicate RID\tExperiment RID\tStudy RID" > rid.tsv
+ echo -e "Replicate\t${repRID}\t${expRID}\t${studyRID}" >> rid.tsv
# make metadata table
echo -e "LOG: creating metadata table" >> ${repRID}.aggrQC.log
echo -e "Source\tSpecies\tEnds\tStranded\tSpike-in\tRaw Reads\tAssigned Reads\tMedian Read Length\tMedian TIN" > metadata.tsv
echo -e "Submitter\t${speciesM}\t${endsM}\t${strandedM}\t${spikeM}\t-\t-\t'${readLengthM}'\t-" >> metadata.tsv
- echo -e "Infered\t${speciesI}\t${endsI}\t${strandedI}\t${spikeI}\t-\t-\t-\t-" >> metadata.tsv
+ if [ "${params.speciesForce}" == "" ]
+ then
+ echo -e "Infered\t${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${spikeI}\t-\t-\t-\t-" >> metadata.tsv
+ fi
echo -e "Measured\t-\t${endsManual}\t-\t-\t'${rawReadsI}'\t'${assignedReadsI}'\t'${readLengthI}'\t'${tinMedI}'" >> metadata.tsv
# make reference table
--
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