Fix Controlfreec: Add stub runs to test single sample input & make conda work with R scripts (#1504)

* Fix typo

* Add stub runs for testing input without matched normals

* Add missing -stub-run

* remove empty file checksum tests and change workflow names

* test controlfreec naming

* fix output file names

* fix output file names

* fix output file names

* fix conda and container path difference for R scripts

* update tar version to work with conda

* fix version number in docker

* try to fix path to script, pretty sure it won't work

* try new ways to set path with wildcard

* try which

* add which but with escape

* remove comment

modules/controlfreec/assesssignificance/main.nf

@@ -21,7 +21,7 @@ process CONTROLFREEC_ASSESSSIGNIFICANCE {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    cat /usr/local/bin/assess_significance.R | R --slave --args ${cnvs} ${ratio}
+    cat \$(which assess_significance.R) | R --slave --args ${cnvs} ${ratio}
 
     mv *.p.value.txt ${prefix}.p.value.txt
 
@@ -30,4 +30,15 @@ process CONTROLFREEC_ASSESSSIGNIFICANCE {
         controlfreec: \$(echo \$(freec -version 2>&1) | sed 's/^.*Control-FREEC  //; s/:.*\$//' | sed -e "s/Control-FREEC v//g" )
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.p.value.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        controlfreec: \$(echo \$(freec -version 2>&1) | sed 's/^.*Control-FREEC  //; s/:.*\$//' | sed -e "s/Control-FREEC v//g" )
+    END_VERSIONS
+    """
 }

modules/controlfreec/freec/main.nf

@@ -21,7 +21,7 @@ process CONTROLFREEC_FREEC {
 
     output:
     tuple val(meta), path("*_ratio.BedGraph")   , emit: bedgraph, optional: true
-    tuple val(meta), path("*_control.cpn")      , emit: control_cpn
+    tuple val(meta), path("*_control.cpn")      , emit: control_cpn, optional: true
     tuple val(meta), path("*_sample.cpn")       , emit: sample_cpn
     tuple val(meta), path("GC_profile.*.cpn")   , emit: gcprofile_cpn, optional:true
     tuple val(meta), path("*_BAF.txt")          , emit: BAF
@@ -155,4 +155,22 @@ process CONTROLFREEC_FREEC {
         controlfreec: \$(echo \$(freec -version 2>&1) | sed 's/^.*Control-FREEC  //; s/:.*\$//' | sed -e "s/Control-FREEC v//g" )
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_ratio.BedGraph
+    touch ${prefix}_sample.cpn
+    touch GC_profile.${prefix}.cpn
+    touch ${prefix}_BAF.txt
+    touch ${prefix}_CNVs
+    touch ${prefix}_info.txt
+    touch ${prefix}_ratio.txt
+    touch config.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        controlfreec: \$(echo \$(freec -version 2>&1) | sed 's/^.*Control-FREEC  //; s/:.*\$//' | sed -e "s/Control-FREEC v//g" )
+    END_VERSIONS
+    """
 }

modules/controlfreec/freec2bed/main.nf

@@ -28,4 +28,15 @@ process CONTROLFREEC_FREEC2BED {
         controlfreec: \$(echo \$(freec -version 2>&1) | sed 's/^.*Control-FREEC  //; s/:.*\$//' | sed -e "s/Control-FREEC v//g" )
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.bed
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        controlfreec: \$(echo \$(freec -version 2>&1) | sed 's/^.*Control-FREEC  //; s/:.*\$//' | sed -e "s/Control-FREEC v//g" )
+    END_VERSIONS
+    """
 }

modules/controlfreec/freec2circos/main.nf

@@ -28,4 +28,15 @@ process CONTROLFREEC_FREEC2CIRCOS {
         controlfreec: \$(echo \$(freec -version 2>&1) | sed 's/^.*Control-FREEC  //; s/:.*\$//' | sed -e "s/Control-FREEC v//g" )
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.circos.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        controlfreec: \$(echo \$(freec -version 2>&1) | sed 's/^.*Control-FREEC  //; s/:.*\$//' | sed -e "s/Control-FREEC v//g" )
+    END_VERSIONS
+    """
 }

modules/controlfreec/makegraph/main.nf

@@ -25,12 +25,24 @@ process CONTROLFREEC_MAKEGRAPH {
     def prefix = task.ext.prefix ?: "${meta.id}"
     def baf = baf ?: ""
     """
-    cat /usr/local/bin/makeGraph.R | R --slave --args ${args} ${ratio} ${baf}
+    cat \$(which makeGraph.R) | R --slave --args ${args} ${ratio} ${baf}
 
     mv *_BAF.txt.png ${prefix}_BAF.png
     mv *_ratio.txt.log2.png ${prefix}_ratio.log2.png
     mv *_ratio.txt.png ${prefix}_ratio.png
 
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        controlfreec: \$(echo \$(freec -version 2>&1) | sed 's/^.*Control-FREEC  //; s/:.*\$//' | sed -e "s/Control-FREEC v//g" )
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_BAF.png
+    touch ${prefix}_ratio.log2.png
+    touch ${prefix}_ratio.png
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/untar/main.nf

@@ -2,10 +2,10 @@ process UNTAR {
     tag "$archive"
     label 'process_low'
 
-    conda (params.enable_conda ? "conda-forge::tar=1.32" : null)
+    conda (params.enable_conda ? "conda-forge::tar=1.34" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :
+        'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv2/biocontainers_v1.2.0_cv2.img' :
-        'biocontainers/biocontainers:v1.2.0_cv1' }"
+        'biocontainers/biocontainers:v1.2.0_cv2' }"
 
     input:
     tuple val(meta), path(archive)

tests/modules/controlfreec/assesssignificance/main.nf

@@ -40,3 +40,38 @@ workflow test_controlfreec_assesssignificance {
     sig_in = CONTROLFREEC_FREEC.out.CNV.join(CONTROLFREEC_FREEC.out.ratio)
     CONTROLFREEC_ASSESSSIGNIFICANCE ( sig_in )
 }
+
+workflow test_controlfreec_assesssignificance_single {
+
+    input = [
+        [ id:'test', single_end:false, sex:'XX' ], // meta map
+        [],
+        file(params.test_data['homo_sapiens']['illumina']['test2_mpileup'], checkIfExists: true),
+        [],[],[],[]
+    ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+
+    dbsnp = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'], checkIfExists: true)
+    dbsnp_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz_tbi'], checkIfExists: true)
+
+    chrfiles = [ [], file(params.test_data['homo_sapiens']['genome']['genome_21_chromosomes_dir'], checkIfExists: true) ]
+    target_bed = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
+
+    UNTAR(chrfiles)
+    CONTROLFREEC_FREEC (input,
+                        fasta,
+                        fai,
+                        [],
+                        dbsnp,
+                        dbsnp_tbi,
+                        UNTAR.out.untar.map{ it[1] },
+                        [],
+                        target_bed,
+                        []
+                        )
+
+    sig_in = CONTROLFREEC_FREEC.out.CNV.join(CONTROLFREEC_FREEC.out.ratio)
+    CONTROLFREEC_ASSESSSIGNIFICANCE ( sig_in )
+}

tests/modules/controlfreec/assesssignificance/test.yml

@@ -7,4 +7,12 @@
     - path: output/controlfreec/test.p.value.txt
       md5sum: 44e23b916535fbc1a3f47b57fad292df
     - path: output/controlfreec/versions.yml
-      md5sum: 0aa42fed10d61e4570fe1e0e83ffe932
+
+- name: controlfreec assesssignificance test_controlfreec_assesssignificance_single
+  command: nextflow run tests/modules/controlfreec/assesssignificance -entry test_controlfreec_assesssignificance_single -c tests/config/nextflow.config -stub-run
+  tags:
+    - controlfreec/assesssignificance
+    - controlfreec
+  files:
+    - path: output/controlfreec/test.p.value.txt
+    - path: output/controlfreec/versions.yml

tests/modules/controlfreec/freec/main.nf

@@ -36,3 +36,36 @@ workflow test_controlfreec_freec {
                         []
                         )
 }
+
+workflow test_controlfreec_freec_single {
+
+    input = [
+        [ id:'test2', single_end:false, sex:'XX' ], // meta map
+        [],
+        file(params.test_data['homo_sapiens']['illumina']['test2_mpileup'], checkIfExists: true),
+        [],[],[],[]
+    ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+
+    dbsnp = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'], checkIfExists: true)
+    dbsnp_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz_tbi'], checkIfExists: true)
+
+    chrfiles = [ [], file(params.test_data['homo_sapiens']['genome']['genome_21_chromosomes_dir'], checkIfExists: true) ]
+    target_bed = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
+
+    UNTAR(chrfiles)
+    CONTROLFREEC_FREEC (input,
+                        fasta,
+                        fai,
+                        [],
+                        dbsnp,
+                        dbsnp_tbi,
+                        UNTAR.out.untar.map{ it[1] },
+                        [],
+                        target_bed,
+                        []
+                        )
+}
+

tests/modules/controlfreec/freec/test.yml

@@ -20,4 +20,18 @@
     - path: output/controlfreec/test2.mpileup.gz_sample.cpn
       md5sum: c80dad58a77b1d7ba6d273999f4b4b4b
     - path: output/controlfreec/versions.yml
-      md5sum: 3ab250a2ab3be22628124c7c65324651
+
+- name: controlfreec test_controlfreec_freec_single
+  command: nextflow run tests/modules/controlfreec/freec -entry test_controlfreec_freec_single -c tests/config/nextflow.config -stub-run
+  tags:
+    - controlfreec
+    - controlfreec/freec
+  files:
+    - path: output/controlfreec/config.txt
+    - path: output/controlfreec/test2_BAF.txt
+    - path: output/controlfreec/test2_CNVs
+    - path: output/controlfreec/test2_info.txt
+    - path: output/controlfreec/test2_ratio.BedGraph
+    - path: output/controlfreec/test2_ratio.txt
+    - path: output/controlfreec/test2_sample.cpn
+    - path: output/controlfreec/versions.yml

tests/modules/controlfreec/freec2bed/main.nf

@@ -39,3 +39,37 @@ workflow test_controlfreec_freec2bed {
 
     CONTROLFREEC_FREEC2BED ( CONTROLFREEC_FREEC.out.ratio )
 }
+
+workflow test_controlfreec_freec2bed_single {
+
+      input = [
+        [ id:'test', single_end:false, sex:'XX' ], // meta map
+        [],
+        file(params.test_data['homo_sapiens']['illumina']['test2_mpileup'], checkIfExists: true),
+        [],[],[],[]
+    ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+
+    dbsnp = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'], checkIfExists: true)
+    dbsnp_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz_tbi'], checkIfExists: true)
+
+    chrfiles = [ [], file(params.test_data['homo_sapiens']['genome']['genome_21_chromosomes_dir'], checkIfExists: true) ]
+    target_bed = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
+
+    UNTAR(chrfiles)
+    CONTROLFREEC_FREEC (input,
+                        fasta,
+                        fai,
+                        [],
+                        dbsnp,
+                        dbsnp_tbi,
+                        UNTAR.out.untar.map{ it[1] },
+                        [],
+                        target_bed,
+                        []
+                        )
+
+    CONTROLFREEC_FREEC2BED ( CONTROLFREEC_FREEC.out.ratio )
+}

tests/modules/controlfreec/freec2bed/test.yml

@@ -6,3 +6,11 @@
   files:
     - path: output/controlfreec/test.bed
       md5sum: abe10b7ce94ba903503e697394c17297
+
+- name: controlfreec freec2bed test_controlfreec_freec2bed_single
+  command: nextflow run tests/modules/controlfreec/freec2bed -entry test_controlfreec_freec2bed_single -c tests/config/nextflow.config -stub-run
+  tags:
+    - controlfreec/freec2bed
+    - controlfreec
+  files:
+    - path: output/controlfreec/test.bed

tests/modules/controlfreec/freec2circos/main.nf

@@ -39,3 +39,37 @@ workflow test_controlfreec_freec2circos {
 
     CONTROLFREEC_FREEC2CIRCOS ( CONTROLFREEC_FREEC.out.ratio )
 }
+
+workflow test_controlfreec_freec2circos_single {
+
+    input = [
+        [ id:'test', single_end:false, sex:'XX' ], // meta map
+        [],
+        file(params.test_data['homo_sapiens']['illumina']['test2_mpileup'], checkIfExists: true),
+        [],[],[],[]
+    ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+
+    dbsnp = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'], checkIfExists: true)
+    dbsnp_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz_tbi'], checkIfExists: true)
+
+    chrfiles = [ [], file(params.test_data['homo_sapiens']['genome']['genome_21_chromosomes_dir'], checkIfExists: true) ]
+    target_bed = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
+
+    UNTAR(chrfiles)
+    CONTROLFREEC_FREEC (input,
+                        fasta,
+                        fai,
+                        [],
+                        dbsnp,
+                        dbsnp_tbi,
+                        UNTAR.out.untar.map{ it[1] },
+                        [],
+                        target_bed,
+                        []
+                        )
+
+    CONTROLFREEC_FREEC2CIRCOS ( CONTROLFREEC_FREEC.out.ratio )
+}

tests/modules/controlfreec/freec2circos/test.yml

@@ -6,3 +6,11 @@
   files:
     - path: output/controlfreec/test.circos.txt
       md5sum: 19cf35f2c36b46f717dc8342b8a5a645
+
+- name: controlfreec freec2circos test_controlfreec_freec2circos_single
+  command: nextflow run tests/modules/controlfreec/freec2circos -entry test_controlfreec_freec2circos_single -c tests/config/nextflow.config -stub-run
+  tags:
+    - controlfreec
+    - controlfreec/freec2circos
+  files:
+    - path: output/controlfreec/test.circos.txt

tests/modules/controlfreec/makegraph/main.nf

@@ -40,3 +40,38 @@ workflow test_controlfreec_makegraph {
     makegraph_in = CONTROLFREEC_FREEC.out.ratio.join(CONTROLFREEC_FREEC.out.BAF)
     CONTROLFREEC_MAKEGRAPH ( makegraph_in )
 }
+
+workflow test_controlfreec_makegraph_single {
+
+    input = [
+        [ id:'test', single_end:false, sex:'XX' ], // meta map
+        [],
+        file(params.test_data['homo_sapiens']['illumina']['test2_mpileup'], checkIfExists: true),
+        [],[],[],[]
+    ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+
+    dbsnp = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'], checkIfExists: true)
+    dbsnp_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz_tbi'], checkIfExists: true)
+
+    chrfiles = [ [], file(params.test_data['homo_sapiens']['genome']['genome_21_chromosomes_dir'], checkIfExists: true) ]
+    target_bed = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
+
+    UNTAR(chrfiles)
+    CONTROLFREEC_FREEC (input,
+                        fasta,
+                        fai,
+                        [],
+                        dbsnp,
+                        dbsnp_tbi,
+                        UNTAR.out.untar.map{ it[1] },
+                        [],
+                        target_bed,
+                        []
+                        )
+
+    makegraph_in = CONTROLFREEC_FREEC.out.ratio.join(CONTROLFREEC_FREEC.out.BAF)
+    CONTROLFREEC_MAKEGRAPH ( makegraph_in )
+}

tests/modules/controlfreec/makegraph/test.yml

@@ -10,3 +10,13 @@
       md5sum: b3c7916b1b4951a0cc3da20d8e9e0262
     - path: output/controlfreec/test_ratio.png
       md5sum: 1435b29536b3b1555b4c423f8f4fb000
+
+- name: controlfreec makegraph test_controlfreec_makegraph_single
+  command: nextflow run tests/modules/controlfreec/makegraph -entry test_controlfreec_makegraph_single -c tests/config/nextflow.config -stub-run
+  tags:
+    - controlfreec
+    - controlfreec/makegraph
+  files:
+    - path: output/controlfreec/test_BAF.png
+    - path: output/controlfreec/test_ratio.log2.png
+    - path: output/controlfreec/test_ratio.png