diff --git a/CHANGELOG.md b/CHANGELOG.md
index 04aeb94818b792677615d2e4bd6baf132fcd6b90..4c53d8a46b173bcb46137bfb82348ba12e175626 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,6 @@
# v.2.x.x (indev)
**User Facing**
+* Corrected spelling of inferred (#125)
**Background**
* Corrected file search parameters due to name inconsistency (#129)
diff --git a/conf/multiqc_config.yaml b/conf/multiqc_config.yaml
index ed1375aed47a454394029e5057695b0c15babd8c..1484c4dbad62d6aaf6c8d995d02723f8b5ccc15f 100644
--- a/conf/multiqc_config.yaml
+++ b/conf/multiqc_config.yaml
@@ -103,7 +103,7 @@ custom_data:
meta:
file_format: 'tsv'
section_name: 'Metadata'
- description: 'This is the comparison of infered metadata, submitter provided, and calculated'
+ description: 'This is the comparison of inferred metadata, submitter provided, and calculated'
plot_type: 'table'
pconfig:
id: 'meta'
diff --git a/rna-seq.nf b/rna-seq.nf
index 159805d91f41c6451eec27db96ef199265f3b07a..305106d3ae1cf0d6d4655d5db94959199641f075 100644
--- a/rna-seq.nf
+++ b/rna-seq.nf
@@ -220,7 +220,7 @@ process getBag {
"""
}
-// Set inputBag to downloaded or forced input and replicate them for multiple process inputs
+// Set inputBag to downloaded or forced input and replicate them for multiple process inputs
if (inputBagForce != "") {
inputBag = Channel
.fromPath(inputBagForce)
@@ -723,7 +723,7 @@ process seqwho {
# get seqwho index
wget -O SeqWho.ix https://cloud.biohpc.swmed.edu/index.php/s/eeNWqZz8jqN5zWY/download
echo -e "LOG: seqwho index downloaded" >> ${repRID}.seqwho.log
-
+
# run seqwho
seqwho.py -f *.fastq.gz -x SeqWho.ix
echo -e "LOG: seqwho ran" >> ${repRID}.seqwho.log
@@ -812,7 +812,7 @@ process seqwho {
echo -e "LOG: concordant species inference: \${speciesInfer}" >> ${repRID}.seqwho.log
else
speciesErrorSeqwho=true
- speciesErrorSeqwho_details="**Infered species does not match for R1 and R2:** Infered R1 = \${speciesR1} and infered R2 = \${speciesR2}"
+ speciesErrorSeqwho_details="**inferred species does not match for R1 and R2:** inferred R1 = \${speciesR1} and inferred R2 = \${speciesR2}"
echo -e "LOG: inference error: \${speciesErrorSeqwho_details}" >> ${repRID}.seqwho.log
fi
@@ -822,8 +822,8 @@ process seqwho {
echo -e "LOG: high confidence species inference detected" >> ${repRID}.seqwho.log
else
speciesErrorSeqwho=true
- speciesErrorSeqwho_details=\$(echo "**Infered species confidence is low:**\\n")
- speciesErrorSeqwho_details=\$(echo \${speciesErrorSeqwho_details}"|fastq|Infered species confidence|\\n")
+ speciesErrorSeqwho_details=\$(echo "**inferred species confidence is low:**\\n")
+ speciesErrorSeqwho_details=\$(echo \${speciesErrorSeqwho_details}"|fastq|inferred species confidence|\\n")
speciesErrorSeqwho_details=\$(echo \${speciesErrorSeqwho_details}"|:--|:--:|\\n")
speciesErrorSeqwho_details=\$(echo \${speciesErrorSeqwho_details}"|Read 1|\${speciesConfidenceR1}|\\n")
if [ "${ends}" == "pe" ]
@@ -846,12 +846,12 @@ process seqwho {
echo -e "LOG: concordant rnaseq seq type inference detected" >> ${repRID}.seqwho.log
else
seqtypeError=true
- seqtypeError_details="**Infered sequencing type is not mRNA-seq:** Infered = \${seqtypeR1}"
+ seqtypeError_details="**inferred sequencing type is not mRNA-seq:** inferred = \${seqtypeR1}"
echo -e "LOG: inference error: \${seqtypeError_details}" >> ${repRID}.seqwho.log
fi
else
seqtypeError=true
- seqtypeError_details="**Infered sequencing type does not match for R1 and R2:** Infered R1 = \${seqtypeR1} and infered R2 = \${seqtypeR2}"
+ seqtypeError_details="**inferred sequencing type does not match for R1 and R2:** inferred R1 = \${seqtypeR1} and inferred R2 = \${seqtypeR2}"
echo -e "LOG: inference error: \${seqtypeError_details}" >> ${repRID}.seqwho.log
fi
consensus="-"
@@ -901,8 +901,8 @@ process seqwho {
if [ \${consensus} == false ]
then
seqtypeError=true
- seqtypeError_details=\$(echo "**Infered sequence-type confidence is low:**\\n")
- seqtypeError_details=\$(echo \${seqtypeError_details}"|fastq|Infered seq type|Infered seq type confidence|\\n")
+ seqtypeError_details=\$(echo "**inferred sequence-type confidence is low:**\\n")
+ seqtypeError_details=\$(echo \${seqtypeError_details}"|fastq|inferred seq type|inferred seq type confidence|\\n")
seqtypeError_details=\$(echo \${seqtypeError_details}"|:--|:--:|:--:|\\n")
seqtypeError_details=\$(echo \${seqtypeError_details}"|Read 1|\${seqtypeR1}|\${seqtypeConfidenceR1}|\\n")
if [ "${ends}" == "pe" ]
@@ -936,7 +936,7 @@ process seqwho {
then
echo -e "Read 2\t\${seqtypeR2}\t\${speciesR2}\t\${seqtypeConfidenceR2}\t\${consensus}\t\${speciesConfidenceR2}" >> seqwhoInfer.tsv
fi
-
+
# save species file
echo "\${speciesInfer}" > inferSpecies.csv
@@ -945,7 +945,7 @@ process seqwho {
"""
}
-// Extract infered sepecies metadata into channel and replicate them for multiple process inputs
+// Extract inferred sepecies metadata into channel and replicate them for multiple process inputs
speciesInfer = Channel.create()
speciesInfer_failPreExecutionRun = Channel.create()
inferSpecies_fl.splitCsv(sep: ",", header: false).separate(
@@ -1581,7 +1581,7 @@ strandedInfer.into {
strandedInfer_failExecutionRun
}
-/*
+/*
* checkMetadata: checks the submitted metadata against inferred
*/
process checkMetadata {
@@ -2192,7 +2192,7 @@ process aggrQC {
"""
}
-/*
+/*
* uploadInputBag: uploads the input bag
*/
process uploadInputBag {
@@ -2230,7 +2230,7 @@ process uploadInputBag {
echo LOG: ${repRID} input bag md5 sum - \${md5} >> ${repRID}.uploadInputBag.log
size=\$(wc -c < ./\${file})
echo LOG: ${repRID} input bag size - \${size} bytes >> ${repRID}.uploadInputBag.log
-
+
exist=\$(curl -s https://${source}/ermrest/catalog/2/entity/RNASeq:Input_Bag/File_MD5=\${md5})
if [ "\${exist}" == "[]" ]
then
@@ -2265,7 +2265,7 @@ inputBagRID.into {
inputBagRID_failExecutionRun
}
-/*
+/*
* uploadExecutionRun: uploads the execution run
*/
process uploadExecutionRun {
@@ -2283,7 +2283,7 @@ process uploadExecutionRun {
val seqtypeError from seqtypeError_uploadExecutionRun
val speciesErrorSeqwho from speciesErrorSeqwho_uploadExecutionRun
val speciesError from speciesError_uploadExecutionRun
-
+
output:
path ("executionRunRID.csv") into executionRunRID_fl
@@ -2370,7 +2370,7 @@ executionRunRID.into {
executionRunRID_fail
}
-/*
+/*
* uploadQC: uploads the mRNA QC
*/
process uploadQC {
@@ -2480,7 +2480,7 @@ process uploadProcessedFile {
script:
"""
-
+
hostname > ${repRID}.uploadProcessedFile.log
ulimit -a >> ${repRID}.uploadProcessedFile.log
@@ -2550,7 +2550,7 @@ process uploadProcessedFile {
"""
}
-/*
+/*
* uploadOutputBag: uploads the output bag
*/
process uploadOutputBag {
@@ -2597,7 +2597,7 @@ process uploadOutputBag {
echo LOG: ${repRID} output bag md5 sum - \${md5} >> ${repRID}.uploadOutputBag.log
size=\$(wc -c < ./\${file})
echo LOG: ${repRID} output bag size - \${size} bytes >> ${repRID}.uploadOutputBag.log
-
+
loc=\$(deriva-hatrac-cli --host ${source} put ./\${file} /hatrac/resources/rnaseq/pipeline/output_bag/study/${studyRID}/replicate/${repRID}/\${file} --parents)
echo LOG: output bag uploaded - \${loc} >> ${repRID}.uploadOutputBag.log
# url-ify the location
@@ -2632,7 +2632,7 @@ outputBagRID_fl.splitCsv(sep: ",", header: false).separate(
outputBagRID
)
-/*
+/*
* finalizeExecutionRun: finalizes the execution run
*/
process finalizeExecutionRun {
@@ -2698,7 +2698,7 @@ errorDetails.into {
}
-/*
+/*
* failPreExecutionRun: fail the execution run prematurely for fastq errors
*/
process failPreExecutionRun {
@@ -2798,7 +2798,7 @@ executionRunRID_preFail_fl.splitCsv(sep: ",", header: false).separate(
executionRunRID_preFail
)
-/*
+/*
* failPreExecutionRun_seqwho: fail the execution run prematurely for seqwho errors
*/
process failPreExecutionRun_seqwho {
@@ -2902,7 +2902,7 @@ executionRunRID_preFailseqwho_fl.splitCsv(sep: ",", header: false).separate(
failExecutionRunRID = executionRunRID_fail.ifEmpty('').mix(executionRunRID_preFail.ifEmpty('').mix(executionRunRID_preFailseqwho.ifEmpty(''))).filter { it != "" }
-/*
+/*
* failExecutionRun: fail the execution run
*/
process failExecutionRun {
@@ -2982,7 +2982,7 @@ process failExecutionRun {
rid=\$(python3 ${script_uploadExecutionRun_failExecutionRun} -r ${repRID} -w \${workflow} -g \${genome} -i ${inputBagRID} -s Error -d "\${pipelineError_details}" -o ${source} -c \${cookie} -u ${executionRunRID})
echo LOG: execution run RID marked as error - \${rid} >> ${repRID}.failExecutionRun.log
fi
-
+
if [ ${params.track} == true ]
then
dt=`date +%FT%T.%3N%:z`
@@ -2997,7 +2997,7 @@ process failExecutionRun {
"""
}
-/*
+/*
* uploadQC_fail: uploads the mRNA QC on failed execution run
*/
process uploadQC_fail {
diff --git a/workflow/conf/multiqc_config.yaml b/workflow/conf/multiqc_config.yaml
index 89059e01682adfcd9354e3c7d78b6a65a87bf569..6dd1cbc262376ab803330a37e6ba36e37ba7e2a7 100644
--- a/workflow/conf/multiqc_config.yaml
+++ b/workflow/conf/multiqc_config.yaml
@@ -103,7 +103,7 @@ custom_data:
meta:
file_format: 'tsv'
section_name: 'Metadata'
- description: 'This is the comparison of infered metadata, submitter provided, and calculated'
+ description: 'This is the comparison of inferred metadata, submitter provided, and calculated'
plot_type: 'table'
pconfig:
id: 'meta'