Merge branch '125-infered' into 'develop'

Changed the spelling of inferred. Closes #125 See merge request !89

Merge branch '125-infered' into 'develop'
Changed the spelling of inferred. Closes #125 See merge request !89
8ba4e7b2 · Gervaise Henry · bb1e0848 · 8ee49ad3 · 8ba4e7b2 · 8ba4e7b2
Commit 8ba4e7b2 authored 3 years ago by Gervaise Henry
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
 # v.2.x.x (indev)
 **User Facing**
+* Corrected spelling of inferred (#125)

 **Background**
 * Corrected file search parameters due to name inconsistency (#129)

--- 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'

--- 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 {

--- 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'