Add software version scrape (#42)

### Added
Software versions file

bin/get_versions.py

@@ -0,0 +1,46 @@
+#!/usr/bin/env python
+import os
+import sys
+import re
+
+version_regex = {
+    "artic": r"artic (\S+)",
+    "bcftools": r"bcftools (\S+)",
+    "bwa": r"Version: (\S+)",
+    "constellations": r"constellations v(\S+)",
+    "fastqc": r"FastQC v(\S+)",
+    "freebayes": r"version:  v(\d\.\d\.\d+)",
+    "gofasta": r"gofasta version (\S+)",
+    "ivar": r"iVar version (\S+)",
+    "mafft": r"v(\S+)",
+    "medaka": r"medaka (\S+)",
+    "minimap2": r"(\S+)",
+    "multiqc": r"multiqc, version (\S+)",
+    "muscle": r"MUSCLE (\S+)",
+    "nanopolish": r"nanopolish version (\S+)",
+    "nextclade": r"(\S+)",
+    "pango_designation": r"pango-designation (\S+)",
+    "pangoLEARN": r"pangoLEARN (\S+)",
+    "pangolin": r"pangolin (\S+)",
+    "picard": r"Version:(\S+)",
+    "porechop": r"(\S+)",
+    "python": r"Python (\S+)",
+    "samtools": r"samtools (\S+)",
+    "scorpio": r"scorpio (\S+)",
+    "snakemake": r"(\S+)",
+    "trim_galore": r"version (\S+)",
+    "usher": r"UShER \((\S+)\)"
+}
+# Create csv file for all versions
+output = sys.argv[1]
+with open(output, "w") as out:
+    for tool, regex in version_regex.items():
+        # Search for version number
+        version_file = "version_{}.txt".format(tool)
+        if os.path.isfile(version_file):
+            with open(version_file) as f:
+                contents = f.read()
+                match = re.search(regex, contents)
+                if match:
+                    # Add version number to output
+                    out.write("{},{}\n".format(tool, match.group(1)))

modules/analysis.nf

@@ -26,3 +26,57 @@ process makeReport {
     makeReport.py ${sampleName}
     """
 }
+
+process versions {
+    publishDir "${params.outdir}/${task.process.replaceAll(":","_")}", pattern: "*", mode: 'copy'
+
+    output:
+    file "*versions.csv"
+
+    script:
+    if ( params.illumina )
+        """
+        bcftools -v > version_bcftools.txt
+        bwa > version_bwa.txt 2>&1 || true
+        scorpio -cv > version_constellations.txt
+        fastqc -v > version_fastqc.txt
+        gofasta -v > version_gofasta.txt
+        freebayes --version > version_freebayes.txt
+        ivar version > version_ivar.txt
+        multiqc --version > version_multiqc.txt
+        nextclade --version > version_nextclade.txt
+        pangolin -dv > version_pango_designation.txt
+        pangolin -pv > version_pangoLEARN.txt
+        pangolin -v > version_pangolin.txt
+        picard CollectWgsMetrics -version > version_picard.txt 2>&1 || true
+        python --version > version_python.txt
+        samtools --version > version_samtools.txt
+        scorpio -v > version_scorpio.txt
+        snakemake -v > version_snakemake.txt
+        trim_galore -v > version_trim_galore.txt
+        usher --version > version_usher.txt
+        get_versions.py ${params.prefix}_versions.csv
+        """
+    else if ( params.medaka || params.nanopolish )
+        """
+        artic --version > version_artic.txt
+        bwa > version_bwa.txt 2>&1 || true
+        scorpio -cv > version_constellations.txt
+        gofasta -v > version_gofasta.txt
+        mafft --version > version_mafft.txt 2>&1
+        medaka --version > version_medaka.txt
+        minimap2 --version > version_minimap2.txt
+        muscle -version > version_muscle.txt
+        nanopolish --version > version_nanopolish.txt
+        nextclade --version > version_nextclade.txt
+        pangolin -dv > version_pango_designation.txt
+        pangolin -pv > version_pangoLEARN.txt
+        pangolin -v > version_pangolin.txt
+        porechop --version > version_porechop.txt
+        python --version > version_python.txt
+        samtools --version > version_samtools.txt
+        scorpio -v > version_scorpio.txt
+        snakemake -v > version_snakemake.txt
+        get_versions.py ${params.prefix}_versions.csv
+        """
+}

nextflow.config

@@ -42,6 +42,16 @@ profiles {
     docker.enabled = true
     fixOwnership = true
     runOptions = "-u \$(id -u):\$(id -g)"
+    if ( params.medaka || params.nanopolish ){
+      process {
+        container="genomicmedicinesweden/gms-artic-nanopore:latest"
+      }
+    }
+    else {
+      process {
+        container="genomicmedicinesweden/gms-artic-illumina:latest"
+      }
+    }
   }
   singularity {
     singularity.enabled = true 
@@ -91,6 +101,9 @@ profiles {
         withName:makeReport {
           container="docker://genomicmedicinesweden/gms-artic-nanopore:latest"
         }
+        withName:versions {
+          container="docker://genomicmedicinesweden/gms-artic-nanopore:latest"
+        }
       }
     } else if (params.illumina) {
         process.container = "docker://genomicmedicinesweden/gms-artic-illumina:latest"

workflows/articNcovNanopore.nf

@@ -17,6 +17,7 @@ include {pangolinTyping} from '../modules/typing.nf'
 include {nextclade} from '../modules/typing.nf'
 include {getVariantDefinitions} from '../modules/analysis.nf'
 include {makeReport} from '../modules/analysis.nf'
+include {versions} from '../modules/analysis.nf'
 
 include {bamToCram} from '../modules/out.nf'
 
@@ -33,8 +34,10 @@ workflow sequenceAnalysisNanopolish {
       ch_seqSummary
 
     main:
+      versions()
+
       articDownloadScheme()
-      
+
       articGuppyPlex(ch_runFastqDirs.flatten())
 
       articMinIONNanopolish(articGuppyPlex.out.fastq

workflows/illuminaNcov.nf

@@ -17,6 +17,7 @@ include {pangolinTyping} from '../modules/typing.nf'
 include {nextclade} from '../modules/typing.nf'
 include {getVariantDefinitions} from '../modules/analysis.nf'
 include {makeReport} from '../modules/analysis.nf'
+include {versions} from '../modules/analysis.nf'
 include {cramToFastq} from '../modules/illumina.nf'
 
 include {makeQCCSV} from '../modules/qc.nf'
@@ -99,6 +100,8 @@ workflow sequenceAnalysis {
       ch_bedFile
 
     main:
+      versions()
+
       fastqc(ch_filePairs)
 
       readTrimming(ch_filePairs)