Merge pull request #25 from B-UMMI/remove_bcalm2

remove BCALM2 from workflow

.github/workflows/ci_nextflow.yml

@@ -23,7 +23,7 @@ jobs:
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile docker --fastq "test/data/tiny_{1,2}.*" \
           --reference "test/data/tiny_reference.fasta" --max_cpus 2 --max_memory 4.GB \
-          --abyss false --bcalm false --gatb_minia false --idba false --metahipmer2 false \
+          --abyss false --gatb_minia false --idba false --metahipmer2 false \
           --minia false --megahit false --metaspades false --spades false --unicycler false \
           --velvetoptimiser false
           FILE=report/index.html 
@@ -50,7 +50,7 @@ jobs:
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile singularity --fastq "test/data/tiny_{1,2}.*" \
           --reference "test/data/tiny_reference.fasta" --max_cpus 2 --max_memory 4.GB \
-          --abyss false --bcalm false --gatb_minia false --idba false --metahipmer2 false \
+          --abyss false --gatb_minia false --idba false --metahipmer2 false \
           --minia false --megahit false --metaspades false --spades false --unicycler false \
           --velvetoptimiser false
           FILE=report/index.html 

conf/containers.config

@@ -1,13 +1,10 @@
 process {
         withName: REFORMAT {
-        container = "pcerqueira/bbtools:38.44"
+            container = "pcerqueira/bbtools:38.44"
         }
         withName: ABYSS {
             container = "cimendes/abyss:2.3.1-1"
         }
-        withName: BCALM2 {
-            container = "cimendes/bcalm:2.2.3-1"
-        }
         withName: GATBMINIAPIPELINE {
             container = "cimendes/gatb-minia-pipeline:31.07.2020-1"
         }

conf/params.config

@@ -17,10 +17,6 @@ params {
         abyssKmerSize = 96
         abyssBloomSize = '2G'
 
-        //BCALM2
-        bcalm = false
-        bcalmKmerSize = 31
-
         //GATB Minia Pipeline
         gatb_minia = true
         gatbKmerSize = '21,61,101,141,181'

lib/CheckParams.groovy

@@ -9,11 +9,10 @@ class Params {
         if (params.fastq instanceof Boolean) {print_error("'--fastq' must be a path pattern. Provided value: '$params.fastq'")}
 
         // assembler skipping
-        if (!params.abyss && !params.bcalm && !params.gatb_minia && !params.idba && !params.metahipmer2 && !params.minia && !params.megahit && !params.metaspades && !params.spades && !params.skesa && !params.unicycler && !params.velvetoptimiser) {print_error("All assembly processes set to false. Exiting.")}
+        if (!params.abyss && !params.gatb_minia && !params.idba && !params.metahipmer2 && !params.minia && !params.megahit && !params.metaspades && !params.spades && !params.skesa && !params.unicycler && !params.velvetoptimiser) {print_error("All assembly processes set to false. Exiting.")}
 
         // assembler parameters
-        if (!params.abyssKmerSize.toString().isNumber()) {print_error("'--bcalmKmerSize' parameter must be a number. Provided value: '$params.abyssKmerSize'")}
-        if (!params.bcalmKmerSize.toString().isNumber()) {print_error("'--bcalmKmerSize' parameter must be a number. Provided value: '$params.bcalmKmerSize'")}
+        if (!params.abyssKmerSize.toString().isNumber()) {print_error("'--abyssKmerSize' parameter must be a number. Provided value: '$params.abyssKmerSize'")}
         if (!params.gatb_besst_iter.toString().isNumber()) {print_error("'--gatb_besst_iter' parameter must be a number. Provided value: '$params.gatb_besst_iter'")}
         if (params.metaspadesKmerSize.toString().split(" ").size() <= 1) {if (params.metaspadesKmerSize.toString() != 'auto') {print_error("'--metaspadesKmerSize' parameter must be a sequence of space separated numbers or 'auto'. Provided value: '$params.metaspadesKmerSize'")}}
         if (params.spadesKmerSize.toString().split(" ").size() <= 1) {if (params.spadesKmerSize.toString() != 'auto'){print_error("'--spadesKmerSize' parameter must be a sequence of space separated numbers or 'auto'. Provided value: '$params.spadesKmerSize'")}}

lib/Helper.groovy

@@ -12,7 +12,6 @@ class Help {
         println ""
         int nsamples = info.fastq / 2
         println " Input FastQ                 : $nsamples"
-        println " Reference file              : $info.referece"
         println " Reports are found in        : ./reports"
         println " Results are found in        : ./results"
         println " Profile                     : $profile"
@@ -65,10 +64,6 @@ class Help {
         println "    --abyssBloomSize           Bloom filter size for the ABySS assembler."
         println "                               It must be a sting with a value and an unit."
         println "                               (default: $params.abyssBloomSize)"
-        println "    --bcalm                    Boolean controling the execution of the BCALM2 assembler."
-        println "                               (default: $params.bcalm)"
-        println "    --bcalmKmerSize            K-mer size for the BCALM2 assembler, as an intiger."
-        println "                               (default $params.bcalmKmerSize)"
         println "    --gatb_minia               Boolean controling the execution of the GATB Minia Pipeline assembler."
         println "                               (default: $params.gatb_minia)"
         println "    --gatbKmerSize             K-mer sizes for the GATB Minia Pipeline assembler."

main.nf

@@ -49,11 +49,7 @@ if (params.containsKey('fastq')) {
     infoMap.put('fastq', file(params.fastq).size())
 }
 if (params.containsKey('reference')) {
-    if (file(params.reference) instanceof LinkedList) {
-        infoMap.put('reference', file(params.reference).size())
-    } else {
-        infoMap.put('fasta', 1)
-    }
+    infoMap.put('reference', file(params.reference).getName())
 }
 
 Help.start_info(infoMap, "$workflow.start", "$workflow.profile", "$workflow.manifest.version")

modules/assembly/assembly.nf

@@ -53,41 +53,6 @@ process ABYSS {
     """
 }
 
-process BCALM2 {
-
-    tag { sample_id }
-    label 'process_assembly'
-    publishDir "results/$sample_id/assembly/bcalm2/"
-
-    when:
-    params.bcalm
-
-    input:
-    tuple val(sample_id), path(fastq) 
-    val KmerSize 
-
-    output:
-    tuple val(sample_id), val('BCALM2'), path('*_BCALM2.fasta'), emit: assembly
-    path('.*version'), emit: version 
-
-    script:
-    """
-    ls -1 $fastq  > list_reads
-    bcalm -version | head -n 1 | awk -F ', ' '{print \$2}' | awk -F ' ' '{print \$2}' | awk -F 'v' '{print \$2}' \
-    > .${sample_id}_BCALM2_version
-    {
-        bcalm -in list_reads -out ${sample_id} -kmer-size $KmerSize
-        mv ${sample_id}.unitigs.fa  ${sample_id}_BCALM2.fasta
-        echo pass > .status
-    } || {
-        echo fail > .status
-        :> ${sample_id}_BCALM2.fasta
-    }
-    # remove temp files
-    rm list_reads *.fa || true
-    """
-}
-
 process GATBMINIAPIPELINE {
 
     tag { sample_id }
@@ -440,7 +405,6 @@ workflow assembly_wf {
 
     abyssKmerSize = Channel.value(params.abyssKmerSize)
     abyssBloomSize = Channel.value(params.abyssBloomSize)
-    bcalmKmerSize = Channel.value(params.bcalmKmerSize)
     gatbKmerSize = Channel.value(params.gatbKmerSize)
     GATB_error_correction = params.gatb_error_correction ? 'true' : 'false'
     gatb_besst_iter = Channel.value(params.gatb_besst_iter)
@@ -456,7 +420,6 @@ workflow assembly_wf {
     main:
     REFORMAT(IN_fastq_raw)
     ABYSS(IN_fastq_raw, abyssKmerSize, abyssBloomSize)
-    BCALM2(IN_fastq_raw, bcalmKmerSize)
     GATBMINIAPIPELINE(IN_fastq_raw, gatbKmerSize, GATB_error_correction, gatb_besst_iter)
     IDBA(REFORMAT.out)
     MEGAHIT(IN_fastq_raw, megahitKmerSize)
@@ -469,8 +432,7 @@ workflow assembly_wf {
     VELVETOPTIMISER(IN_fastq_raw)
 
     emit:
-    all_assemblies = ABYSS.out.assembly | mix(BCALM2.out.assembly, 
-                                              GATBMINIAPIPELINE.out.assembly,
+    all_assemblies = ABYSS.out.assembly | mix(GATBMINIAPIPELINE.out.assembly,
                                               IDBA.out.assembly,
                                               MEGAHIT.out.assembly,
                                               METAHIPMER2.out.assembly,
@@ -480,8 +442,7 @@ workflow assembly_wf {
                                               SPADES.out.assembly,
                                               UNICYCLER.out.assembly,
                                               VELVETOPTIMISER.out.assembly)
-    all_versions = ABYSS.out.version | mix(BCALM2.out.version, 
-                                           GATBMINIAPIPELINE.out.version,
+    all_versions = ABYSS.out.version | mix(GATBMINIAPIPELINE.out.version,
                                            IDBA.out.version,
                                            MEGAHIT.out.version,
                                            METAHIPMER2.out.version,