update picard/crosscheckfingerprints (nf-core#5077)

* update picard/crosscheckfingerprints * Update modules/nf-core/picard/crosscheckfingerprints/main.nf Co-authored-by: Maxime U Garcia <[email protected]> * fix linting * prettier * add input indexes --------- Co-authored-by: Maxime U Garcia <[email protected]>
LouisLeNezet · Mar 13, 2024 · 5154596 · 5154596
1 parent c6df797
commit 5154596
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Showing 10 changed files with 182 additions and 44 deletions.
diff --git a/modules/nf-core/picard/crosscheckfingerprints/main.nf b/modules/nf-core/picard/crosscheckfingerprints/main.nf
@@ -8,9 +8,8 @@ process PICARD_CROSSCHECKFINGERPRINTS {
         'biocontainers/picard:3.1.1--hdfd78af_0' }"
 
     input:
-    tuple val(meta), path(input1)
-    path input2
-    path haplotype_map
+    tuple val(meta),  path(input1), path(input1_index), path(input2), path(input2_index), path(haplotype_map)
+    tuple val(meta2), path(fasta)
 
     output:
     tuple val(meta), path("*.crosscheck_metrics.txt"), emit: crosscheck_metrics
@@ -23,8 +22,9 @@ process PICARD_CROSSCHECKFINGERPRINTS {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
 
-    def input1_string = input1.join(" --INPUT ")
-    def input2_string = input2 ? "--SECOND_INPUT " + input2.join(" --SECOND_INPUT ") : ""
+    def input1_cmd = input1.collect{"--INPUT $it"}.join(' ')
+    def input2_cmd = input2.collect{"--SECOND_INPUT $it"}.join(' ')
+    def reference_cmd = fasta ? "--REFERENCE_SEQUENCE $fasta" : ""
 
     def avail_mem = 3072
     if (!task.memory) {
@@ -36,16 +36,29 @@ process PICARD_CROSSCHECKFINGERPRINTS {
     picard \\
         -Xmx${avail_mem}M \\
         CrosscheckFingerprints \\
-        $args \\
-        --NUM_THREADS ${task.cpus} \\
-        --INPUT $input1_string \\
-        $input2_string \\
+        ${input1_cmd} \\
+        ${input2_cmd} \\
+        ${reference_cmd} \\
         --HAPLOTYPE_MAP ${haplotype_map} \\
-        --OUTPUT ${prefix}.crosscheck_metrics.txt
+        --OUTPUT ${prefix}.crosscheck_metrics.txt \\
+        --NUM_THREADS ${task.cpus} \\
+        $args
+
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         picard: \$( picard CrosscheckFingerprints --version 2>&1 | grep -o 'Version:.*' | cut -f2- -d: )
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.crosscheck_metrics.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        picard: \$(echo \$(picard CollectHsMetrics --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/picard/crosscheckfingerprints/meta.yml b/modules/nf-core/picard/crosscheckfingerprints/meta.yml
@@ -25,28 +25,50 @@ input:
       type: file
       description: List containing 1 or more bam/vcf files or a file containing filepaths
       pattern: "*.{bam,vcf,vcf.gz,txt,fofn}"
+  - input1_index:
+      type: file
+      description: List containing 1 or more bam/vcf files indexes
+      pattern: "*.{bai,csi,crai,tbi}"
   - input2:
       type: file
       description: Optional list containing 1 or more bam/vcf files or a file containing filepaths
       pattern: "*.{bam,vcf,vcf.gz,txt,fofn}"
+  - input2_index:
+      type: file
+      description: List containing 1 or more bam/vcf files indexes
+      pattern: "*.{bai,csi,crai,tbi}"
   - haplotype_map:
       type: file
       description: Haplotype map file
       pattern: "*.{txt,vcf,vcf.gz}"
+  - meta2:
+      type: map
+      description: |
+        Groovy Map containing reference information
+        e.g. [ id:'genome' ]
+  - fasta:
+      type: file
+      description: Reference genome file
+      pattern: "*.{fasta,fa,fasta.gz,fa.gz}"
+  - fasta_index:
+      type: file
+      description: Reference genome index file
+      pattern: "*.{fai,fasta.fai,fa.fai,fasta.gz.fai,fa.gz.fai}"
 output:
   - meta:
       type: map
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
   - crosscheck_metrics:
       type: file
       description: Metrics created by crosscheckfingerprints
       pattern: "*.{crosscheck_metrics.txt}"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
 authors:
   - "@matthdsm"
 maintainers:

diff --git a/modules/nf-core/picard/crosscheckfingerprints/tests/main.nf.test b/modules/nf-core/picard/crosscheckfingerprints/tests/main.nf.test
@@ -0,0 +1,82 @@
+nextflow_process {
+
+    name "Test Process PICARD_CROSSCHECKFINGERPRINTS"
+    script "../main.nf"
+    config "./nextflow.config"
+
+    process "PICARD_CROSSCHECKFINGERPRINTS"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "picard"
+    tag "picard/crosscheckfingerprints"
+
+    test("homo sapiens - bam - index") {
+        when {
+            process {
+                """
+                input[0] = [
+                            [ id:'test', single_end:false ], //meta
+                            [
+                                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+                                file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true)
+                            ],  // input1
+                            [
+                                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+                                file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true)
+                            ], // input1_index
+                            [], // input2
+                            [], // input2_index
+                            file(params.test_data['homo_sapiens']['genome']['haplotype_map'], checkIfExists: true) // haplotype_map
+                        ]
+                input[1] = [[:],[]]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(file(process.out.crosscheck_metrics[0][1]).name).match("Crosscheck - bam") },
+                { assert snapshot(process.out.versions).match("Crosscheck versions - bam") }
+            )
+        }
+    }
+
+    test("homo sapiens - bam - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                            [ id:'test', single_end:false ], //meta
+                            [
+                                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+                                file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true)
+                            ],  // input1
+                            [
+                                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+                                file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true)
+                            ], // input1_index
+                            [], // input2
+                            [], // input2_index
+                            file(params.test_data['homo_sapiens']['genome']['haplotype_map'], checkIfExists: true) // haplotype_map
+                        ]
+                input[1] = [[:],[]]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(file(process.out.crosscheck_metrics[0][1]).name).match("Crosscheck stub") },
+                { assert snapshot(process.out.versions).match("Crosscheck versions stub") }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/picard/crosscheckfingerprints/tests/main.nf.test.snap b/modules/nf-core/picard/crosscheckfingerprints/tests/main.nf.test.snap
diff --git a/modules/nf-core/picard/crosscheckfingerprints/tests/nextflow.config b/modules/nf-core/picard/crosscheckfingerprints/tests/nextflow.config
@@ -0,0 +1,3 @@
+process {
+    withName: PICARD_CROSSCHECKFINGERPRINTS {ext.args = "--EXIT_CODE_WHEN_MISMATCH 0"}
+}
diff --git a/modules/nf-core/picard/crosscheckfingerprints/tests/tags.yml b/modules/nf-core/picard/crosscheckfingerprints/tests/tags.yml
@@ -0,0 +1,2 @@
+picard/crosscheckfingerprints:
+  - "modules/nf-core/picard/crosscheckfingerprints/**"
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -1649,9 +1649,6 @@ picard/collectwgsmetrics:
 picard/createsequencedictionary:
   - modules/nf-core/picard/createsequencedictionary/**
   - tests/modules/nf-core/picard/createsequencedictionary/**
-picard/crosscheckfingerprints:
-  - modules/nf-core/picard/crosscheckfingerprints/**
-  - tests/modules/nf-core/picard/crosscheckfingerprints/**
 picard/fastqtosam:
   - modules/nf-core/picard/fastqtosam/**
   - tests/modules/nf-core/picard/fastqtosam/**

diff --git a/tests/modules/nf-core/picard/crosscheckfingerprints/main.nf b/tests/modules/nf-core/picard/crosscheckfingerprints/main.nf
diff --git a/tests/modules/nf-core/picard/crosscheckfingerprints/nextflow.config b/tests/modules/nf-core/picard/crosscheckfingerprints/nextflow.config
diff --git a/tests/modules/nf-core/picard/crosscheckfingerprints/test.yml b/tests/modules/nf-core/picard/crosscheckfingerprints/test.yml
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		picard/crosscheckfingerprints:
		- "modules/nf-core/picard/crosscheckfingerprints/**"