added fasta_fai as input + changed if statements

modules/cnvkit/batch/main.nf

@@ -10,6 +10,7 @@ process CNVKIT_BATCH {
     input:
     tuple val(meta), path(tumor), path(normal)
     path  fasta
+    path  fasta_fai
     path  targets
     path  reference
 
@@ -34,12 +35,15 @@ process CNVKIT_BATCH {
     // execute samtools only when cram files are input, cnvkit runs natively on bam but is prohibitively slow
     def tumor_cram = tumor_exists && tumor.Extension == "cram" ? true : false
     def normal_cram = normal_exists && normal.Extension == "cram" ? true : false
+    def tumor_bam = tumor_exists && tumor.Extension == "bam" ? true : false
+    def normal_bam = normal_exists && normal.Extension == "bam" ? true : false
 
     def tumor_out = tumor_cram ? tumor.BaseName + ".bam" : "${tumor}"
 
     // tumor_only mode does not need fasta & target
     // instead it requires a pre-computed reference.cnn which is built from fasta & target
     def (normal_out, normal_args, fasta_args) = ["", "", ""]
+    def fai_reference = fasta_fai ? "--fai-reference ${fasta_fai}" : ""
 
     if (normal_exists){
         def normal_prefix = normal.BaseName
@@ -48,9 +52,9 @@ process CNVKIT_BATCH {
 
         // germline mode
         // normal samples must be input without a flag
-        // requires flag --normal to be empty
+        // requires flag --normal to be empty []
         if(!tumor_exists){
-            tumor_out = normal.BaseName + ".bam"
+            tumor_out = "${normal_prefix}" + ".bam"
             normal_args = "--normal "
         }
         // somatic mode
@@ -62,28 +66,130 @@ process CNVKIT_BATCH {
     def target_args = targets ? "--targets $targets" : ""
     def reference_args = reference ? "--reference $reference" : ""
 
-    """
+    // somatic_mode cram_input
-    if $tumor_cram; then
+    if (tumor_cram && normal_cram){
-        samtools view -T $fasta $tumor -@ $task.cpus -o $tumor_out
+        """
-    fi
+        samtools view -T $fasta $fai_reference $tumor -@ $task.cpus -o $tumor_out
-    if $normal_cram; then
+        samtools view -T $fasta $fai_reference $normal -@ $task.cpus -o $normal_out
-        samtools view -T $fasta $normal -@ $task.cpus -o $normal_out
-    fi
 
+        cnvkit.py \\
+            batch \\
+            $tumor_out \\
+            $normal_args \\
+            $fasta_args \\
+            $reference_args \\
+            $target_args \\
+            --processes $task.cpus \\
+            $args
 
-    cnvkit.py \\
+        cat <<-END_VERSIONS > versions.yml
-        batch \\
+        "${task.process}":
-        $tumor_out \\
+            samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-        $normal_args \\
+            cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g")
-        $fasta_args \\
+        END_VERSIONS
-        $reference_args \\
+        """
-        $target_args \\
+    }
-        --processes $task.cpus \\
+    // somatic_mode bam_input
-        $args
+    else if (tumor_bam && normal_bam){
+        """
+        cnvkit.py \\
+            batch \\
+            $tumor_out \\
+            $normal_args \\
+            $fasta_args \\
+            $reference_args \\
+            $target_args \\
+            --processes $task.cpus \\
+            $args
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g")
+        END_VERSIONS
+        """
+    }
+    // tumor_only_mode cram_input
+    else if(tumor_cram && !normal_exists){
+        """
+        samtools view -T $fasta $fai_reference $tumor -@ $task.cpus -o $tumor_out
+
+        cnvkit.py \\
+            batch \\
+            $tumor_out \\
+            $normal_args \\
+            $fasta_args \\
+            $reference_args \\
+            $target_args \\
+            --processes $task.cpus \\
+            $args
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+            cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g")
+        END_VERSIONS
+        """
+    }
+    // tumor_only bam_input
+    else if(tumor_bam && !normal_exists){
+        """
+        cnvkit.py \\
+            batch \\
+            $tumor_out \\
+            $normal_args \\
+            $fasta_args \\
+            $reference_args \\
+            $target_args \\
+            --processes $task.cpus \\
+            $args
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g")
+        END_VERSIONS
+        """
+    }
+    // germline mode cram_input
+    // normal_args must be --normal []
+    else if (normal_cram && !tumor_exists){
+        """
+        samtools view -T $fasta $fai_reference $normal -@ $task.cpus -o $tumor_out
+
+        cnvkit.py \\
+            batch \\
+            $tumor_out \\
+            $normal_args \\
+            $fasta_args \\
+            $reference_args \\
+            $target_args \\
+            --processes $task.cpus \\
+            $args
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+            cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g")
+        END_VERSIONS
+        """
+    }
+    // germline mode bam_input
+    else if (normal_bam && !tumor_exists){
+        """
+        cnvkit.py \\
+            batch \\
+            $tumor_out \\
+            $normal_args \\
+            $fasta_args \\
+            $reference_args \\
+            $target_args \\
+            --processes $task.cpus \\
+            $args
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g")
+        END_VERSIONS
+        """
+    }
 
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g")
-    END_VERSIONS
-    """
 }

modules/cnvkit/batch/meta.yml

@@ -29,6 +29,10 @@ input:
       type: file
       description: |
         Input reference genome fasta file (only needed for cram_input and/or when normal_samples are provided)
+  - fasta_fai:
+      type: file
+      description: |
+        Input reference genome fasta index (optional, but recommended for cram_input)
   - targetfile:
       type: file
       description: |

tests/modules/cnvkit/batch/main.nf

@@ -7,7 +7,7 @@ include { CNVKIT_BATCH as CNVKIT_WGS       } from '../../../../modules/cnvkit/ba
 include { CNVKIT_BATCH as CNVKIT_TUMORONLY } from '../../../../modules/cnvkit/batch/main.nf'
 include { CNVKIT_BATCH as CNVKIT_GERMLINE } from '../../../../modules/cnvkit/batch/main.nf'
 
-workflow test_cnvkit_hybrid {
+workflow test_cnvkit_hybrid_somatic {
 
     input = [
         [ id:'test' ], // meta map
@@ -17,10 +17,10 @@ workflow test_cnvkit_hybrid {
     fasta   = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
     targets = file(params.test_data['sarscov2']['genome']['baits_bed'], checkIfExists: true)
 
-    CNVKIT_HYBRID ( input, fasta, targets, [] )
+    CNVKIT_HYBRID ( input, fasta, [], targets, [] )
 }
 
-workflow test_cnvkit_wgs {
+workflow test_cnvkit_wgs_somatic {
 
     input = [
         [ id:'test'], // meta map
@@ -29,22 +29,24 @@ workflow test_cnvkit_wgs {
     ]
     fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
 
-    CNVKIT_WGS ( input, fasta, [], [] )
+    CNVKIT_WGS ( input, fasta, [], [], [] )
 }
 
-workflow test_cnvkit_cram {
+workflow test_cnvkit_cram_wgs_somatic {
 
     input = [
         [ id:'test'], // meta map
         file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_cram'], checkIfExists: true),
         file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true)
     ]
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fasta     = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fasta_fai     = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
 
-    CNVKIT_WGS ( input, fasta, [], [] )
+    CNVKIT_WGS ( input, fasta, fasta_fai, [], [] )
 }
 
-workflow test_cnvkit_tumoronly {
+
+workflow test_cnvkit_tumoronly_hybrid_bam {
 
     input = [
         [ id:'test'], // meta map
@@ -53,10 +55,10 @@ workflow test_cnvkit_tumoronly {
     ]
     reference = file(params.test_data['homo_sapiens']['genome']['genome_21_reference_cnn'], checkIfExists: true)
 
-    CNVKIT_TUMORONLY ( input, [], [], reference )
+    CNVKIT_TUMORONLY ( input, [], [],  [], reference )
 }
 
-workflow test_cnvkit_tumoronly_cram {
+workflow test_cnvkit_tumoronly_hybrid_cram {
 
     input = [
         [ id:'test'], // meta map
@@ -66,10 +68,10 @@ workflow test_cnvkit_tumoronly_cram {
     fasta     = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
     reference = file(params.test_data['homo_sapiens']['genome']['genome_21_reference_cnn'], checkIfExists: true)
 
-    CNVKIT_TUMORONLY ( input, fasta, [], reference )
+    CNVKIT_TUMORONLY ( input, fasta, [], [], reference )
 }
 
-workflow test_cnvkit_germline_cram {
+workflow test_cnvkit_germline_hybrid_cram {
 
     input = [
         [ id:'test'], // meta map
@@ -77,7 +79,21 @@ workflow test_cnvkit_germline_cram {
         file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true)
     ]
     fasta     = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
-    targets = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
+    fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+    targets   = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
 
-    CNVKIT_GERMLINE ( input, fasta, targets,  [])
+    CNVKIT_GERMLINE ( input, fasta, fasta_fai, targets,  [])
+}
+
+workflow test_cnvkit_germline_hybrid_bam {
+
+    input = [
+        [ id:'test'], // meta map
+        [],
+        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true)
+    ]
+    fasta     = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+    targets   = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
+
+    CNVKIT_GERMLINE ( input, fasta, [], targets,  [])
 }

tests/modules/cnvkit/batch/test.yml

@@ -1,5 +1,5 @@
-- name: cnvkit batch test_cnvkit_hybrid
+- name: cnvkit batch test_cnvkit_hybrid_somatic
-  command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_hybrid -c ./tests/config/nextflow.config  -c ./tests/modules/cnvkit/batch/nextflow.config
+  command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_hybrid_somatic -c ./tests/config/nextflow.config  -c ./tests/modules/cnvkit/batch/nextflow.config
   tags:
     - cnvkit
     - cnvkit/batch
@@ -26,8 +26,8 @@
     - path: output/cnvkit/test.single_end.sorted.targetcoverage.cnn
       md5sum: aa8a018b1d4d1e688c9f9f6ae01bf4d7
 
-- name: cnvkit batch test_cnvkit_wgs
+- name: cnvkit batch test_cnvkit_wgs_somatic
-  command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_wgs -c ./tests/config/nextflow.config  -c ./tests/modules/cnvkit/batch/nextflow.config
+  command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_wgs_somatic -c ./tests/config/nextflow.config  -c ./tests/modules/cnvkit/batch/nextflow.config
   tags:
     - cnvkit
     - cnvkit/batch
@@ -56,8 +56,8 @@
     - path: output/cnvkit/test2.paired_end.sorted.targetcoverage.cnn
       md5sum: 6ae6b3fce7299eedca6133d911c38fe1
 
-- name: cnvkit batch test_cnvkit_cram
+- name: cnvkit batch test_cnvkit_cram_wgs_somatic
-  command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_cram -c ./tests/config/nextflow.config  -c ./tests/modules/cnvkit/batch/nextflow.config
+  command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_cram_wgs_somatic -c ./tests/config/nextflow.config  -c ./tests/modules/cnvkit/batch/nextflow.config
   tags:
     - cnvkit
     - cnvkit/batch
@@ -86,8 +86,8 @@
     - path: output/cnvkit/test2.paired_end.sorted.targetcoverage.cnn
       md5sum: 6ae6b3fce7299eedca6133d911c38fe1
 
-- name: cnvkit batch test_cnvkit_tumoronly
+- name: cnvkit batch test_cnvkit_tumoronly_hybrid_bam
-  command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_tumoronly -c ./tests/config/nextflow.config  -c ./tests/modules/cnvkit/batch/nextflow.config
+  command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_tumoronly_hybrid_bam -c ./tests/config/nextflow.config  -c ./tests/modules/cnvkit/batch/nextflow.config
   tags:
     - cnvkit
     - cnvkit/batch
@@ -109,8 +109,8 @@
     - path: output/cnvkit/test2.paired_end.recalibrated.sorted.targetcoverage.cnn
       md5sum: e6d0190c1c37ce6e41f76ca5b24ccca3
 
-- name: cnvkit batch test_cnvkit_tumoronly_cram
+- name: cnvkit batch test_cnvkit_tumoronly_hybrid_cram
-  command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_tumoronly_cram -c ./tests/config/nextflow.config  -c ./tests/modules/cnvkit/batch/nextflow.config
+  command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_tumoronly_hybrid_cram -c ./tests/config/nextflow.config  -c ./tests/modules/cnvkit/batch/nextflow.config
   tags:
     - cnvkit
     - cnvkit/batch
@@ -132,8 +132,33 @@
     - path: output/cnvkit/test2.paired_end.recalibrated.sorted.targetcoverage.cnn
       md5sum: e6d0190c1c37ce6e41f76ca5b24ccca3
 
-- name: cnvkit batch test_cnvkit_germline_cram
+- name: cnvkit batch test_cnvkit_germline_hybrid_cram
-  command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_germline_cram -c ./tests/config/nextflow.config  -c ./tests/modules/cnvkit/batch/nextflow.config
+  command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_germline_hybrid_cram -c ./tests/config/nextflow.config  -c ./tests/modules/cnvkit/batch/nextflow.config
+  tags:
+    - cnvkit
+    - cnvkit/batch
+  files:
+    - path: output/cnvkit/multi_intervals.antitarget.bed
+      md5sum: 3d4d20f9f23b39970865d29ef239d20b
+    - path: output/cnvkit/multi_intervals.target.bed
+      md5sum: 86d30493bb2e619a93f4ebc2923d29f3
+    - path: output/cnvkit/reference.cnn
+      md5sum: a09ee4be5dda1cf0f68073bdb3aad8ec
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.antitargetcoverage.cnn
+      md5sum: 067115082c4af4b64d58c0dc3a3642e4
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.bintest.cns
+      md5sum: 68b62b75cd91b2ffe5633686fb943490
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.call.cns
+      md5sum: df196edd72613c59186f4d87df3dc4a4
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.cnr
+      md5sum: 3b4fc0cc73be78f978cfe2422470753e
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.cns
+      md5sum: 4e67451dbcb6601fc3fa5dd7e570f1d4
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.targetcoverage.cnn
+      md5sum: b4a49faf170e436ec32dcc21ccc3ce8f
+
+- name: cnvkit batch test_cnvkit_germline_hybrid_bam
+  command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_germline_hybrid_bam -c ./tests/config/nextflow.config  -c ./tests/modules/cnvkit/batch/nextflow.config
   tags:
     - cnvkit
     - cnvkit/batch