Reply @sateeshperi review. Still missing local modules tests

nf-core · Oct 28, 2024 · 6389825 · 6389825
1 parent 7fbaf48
commit 6389825
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Showing 8 changed files with 40 additions and 42 deletions.
diff --git a/main.nf b/main.nf
@@ -40,10 +40,6 @@ workflow NFCORE_FASTQREPAIR {
     FASTQREPAIR (
         samplesheet
     )
-
-    // emit:
-    // multiqc_report = FASTQREPAIR.out.multiqc_report // channel: /path/to/multiqc_report.html
-
 }
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

diff --git a/modules/local/bbmaprepair/main.nf b/modules/local/bbmaprepair/main.nf
@@ -17,14 +17,10 @@ process BBMAPREPAIR {
         task.ext.when == null || task.ext.when
 
     script:
-        def args = task.ext.args ?: ''
-        def prefix = task.ext.prefix ?: "${meta.id}"
-
         def infastq1 = fastq[0]
         def infastq2 = fastq[1]
         def outfastq1 = infastq1.baseName
         def outfastq2 = infastq2.baseName
-
         """
         repair.sh qin=${params.qin} in=${infastq1} in2=${infastq2} out=${outfastq1}_interleaving.fastq.gz out2=${outfastq2}_interleaving.fastq.gz outsingle=${fastq[0].baseName}_singletons.fastq.gz 2> ${fastq[0].baseName}_repair.log
 
@@ -35,9 +31,6 @@ process BBMAPREPAIR {
     """
 
     stub:
-        def args = task.ext.args ?: ''
-        def prefix = task.ext.prefix ?: "${meta.id}"
-
         def infastq1 = fastq[0]
         def infastq2 = fastq[1]
         def outfastq1 = infastq1.baseName

diff --git a/modules/local/gzrt/main.nf b/modules/local/gzrt/main.nf
@@ -14,10 +14,7 @@ process GZRT {
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
     def filename = "${fastqgz.baseName}"
-
     """
     ver_line=""
     if [[ $fastqgz == *.fastq ]] || [[ $fastqgz == *.fq ]]; then
@@ -35,8 +32,7 @@ process GZRT {
     """
 
     stub:
-    def args = task.ext.args ?: ''
-
+    def filename = "${fastqgz.baseName}"
     """
     ver_line=""
     if [[ $fastqgz == *.fastq ]] || [[ $fastqgz == *.fq ]]; then

diff --git a/modules/local/renamer/main.nf b/modules/local/renamer/main.nf
@@ -15,8 +15,8 @@ process RENAMER {
     task.ext.when == null || task.ext.when
 
     script:
-        def args = task.ext.args ?: ''
-        def prefix = task.ext.prefix ?: "${meta_fastq.id}"
+        def VERSION = '1.0.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+
         def fq1 = fastq[0]
         def fq2 = fastq[1]
 
@@ -66,20 +66,27 @@ process RENAMER {
 
         cat <<-END_VERSIONS > versions.yml
         "${task.process}":
-            renamer: 1.0.0
+        renamer: $VERSION
         END_VERSIONS
     """
 
     stub:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta_fastq.id}"
+    def VERSION = '1.0.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+
     def fq1 = fastq[0]
-    def fq2 = fastq[1]
     def new_name_fq1 = "${meta_fastq.id}_R1_repaired.fastq.gz"
     def new_name_fq2 = "${meta_fastq.id}_R2_repaired.fastq.gz"
     def new_name_fqsingle = "${meta_fastq.id}_repaired.fastq.gz"
+    def is_single_end_fq = "${meta_fastq.single_end}".toBoolean()
+
+    def rep1 = report[0]
+    def new_name_rep1 = "${meta_report.id}_R1_report.txt"
+    def new_name_rep2 = "${meta_report.id}_R2_report.txt"
+    def new_name_repsingle = "${meta_report.id}_report.txt"
+    def is_single_end_report = "${meta_report.single_end}".toBoolean()
 
     """
+        # Rename FASTQ files
         if [[ ${is_single_end_fq} = true ]]; then
             # No second file, treat as single-end
             touch ${new_name_fqsingle}
@@ -95,9 +102,24 @@ process RENAMER {
             touch "${new_name_fq2}"
         fi
 
+        # Rename REPORT files
+        if [[ ${is_single_end_report} = true ]]; then
+            touch ${new_name_repsingle}
+        elif [[ "${rep1}" == *"R2.fastq_recovered_merged_report.txt" ]]; then
+            new_name_rep1="${meta_report.id}_R2_report.txt"
+            new_name_rep2="${meta_report.id}_R1_report.txt"
+            touch "${new_name_rep1}"
+            touch "${new_name_rep2}"
+        elif [[ "${rep1}" == *"R1.fastq_recovered_merged_report.txt" ]]; then
+            new_name_rep2="${meta_report.id}_R2_report.txt"
+            new_name_rep1="${meta_report.id}_R1_report.txt"
+            touch "${new_name_rep1}"
+            touch "${new_name_rep2}"
+        fi
+
         cat <<-END_VERSIONS > versions.yml
         "${task.process}":
-            renamer: 1.0.0
+        renamer: $VERSION
         END_VERSIONS
         """
 }
diff --git a/modules/local/wipertools/gather.nf b/modules/local/wipertools/gather.nf
@@ -5,7 +5,7 @@ process GATHER {
 
     input:
         tuple val(filename), val(meta), path(fastq_list)
-        tuple val(filename), val(meta), path(report_list)
+        tuple val(report_filename), val(report_meta), path(report_list)
 
     output:
         tuple val(meta), path("*merged_wiped.fastq.gz"), emit: fastq_merged_fixed
@@ -16,32 +16,28 @@ process GATHER {
     task.ext.when == null || task.ext.when
 
     script:
-        def args    = task.ext.args ?: ''
-        def prefix  = task.ext.prefix ?: "${meta.id}"
-        def VERSION = '1.0.0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+        def VERSION = '1.0.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
 
         """
         cat ${fastq_list} > ${filename}_merged_wiped.fastq.gz
         wipertools summarygather -s ${report_list} -f ${filename}_merged_report.txt
 
         cat <<-END_VERSIONS > versions.yml
         "${task.process}":
-            wipertools: $VERSION
+        wipertools: $VERSION
         END_VERSIONS
         """
 
     stub:
-        def args = task.ext.args ?: ''
-        def prefix = task.ext.prefix ?: "${meta.id}"
-        def VERSION = '1.0.0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+        def VERSION = '1.0.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
 
         """
         gzip < /dev/null > ${filename}_merged_wiped.fastq.gz
         touch ${filename}_merged_report.txt
 
         cat <<-END_VERSIONS > versions.yml
         "${task.process}":
-            wipertools: $VERSION
+        wipertools: $VERSION
         END_VERSIONS
         """
 }
diff --git a/modules/local/wipertools/scatter.nf b/modules/local/wipertools/scatter.nf
@@ -9,14 +9,11 @@ process SCATTER {
     tuple val(meta), path("*_chunk.*.fastq"), emit: fastq_chunks
     path "versions.yml"                     , emit: versions
 
-    // when:
-    // task.max_cpus > 1
-
     script:
         def args = task.ext.args ?: ''
         def prefix = task.ext.prefix ?: "${meta.id}"
         def filename = "${fastq.baseName}"
-        def VERSION = '1.0.0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+        def VERSION = '1.0.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
 
         """
         split -a3 -l ${params.chunk_size} --numeric-suffixes=1 --additional-suffix .fastq ${fastq} ${filename}_chunk.
@@ -31,7 +28,7 @@ process SCATTER {
         def args = task.ext.args ?: ''
         def prefix = task.ext.prefix ?: "${meta.id}"
         def filename = "${fastq.baseName}"
-        def VERSION = '1.0.0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+        def VERSION = '1.0.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
 
         """
         touch ${filename}_chunk.001.fastq

diff --git a/modules/local/wipertools/wipe.nf b/modules/local/wipertools/wipe.nf
@@ -17,7 +17,7 @@ process WIPER {
     script:
         def args = task.ext.args ?: ''
         def filename = "${fastq.baseName}"
-        def VERSION = '1.0.0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+        def VERSION = '1.0.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
         def log_freq = (params.chunk_size / 100 as Integer) * 10
         log_freq = log_freq == 0 ? 1 : log_freq
 
@@ -33,7 +33,7 @@ process WIPER {
     stub:
         def args = task.ext.args ?: ''
         def filename = "${fastq.baseName}"
-        def VERSION = '1.0.0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+        def VERSION = '1.0.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
         """
         touch ${filename}_wiped.fastq.gz
         touch ${filename}_report.txt

diff --git a/subworkflows/local/utils_nfcore_fastqrepair_pipeline/main.nf b/subworkflows/local/utils_nfcore_fastqrepair_pipeline/main.nf
@@ -114,7 +114,6 @@ workflow PIPELINE_COMPLETION {
     outdir          //    path: Path to output directory where results will be published
     monochrome_logs // boolean: Disable ANSI colour codes in log output
     hook_url        //  string: hook URL for notifications
-    // multiqc_report  //  string: Path to MultiQC report
 
     main:
     summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
@@ -130,8 +129,7 @@ workflow PIPELINE_COMPLETION {
                 email_on_fail,
                 plaintext_email,
                 outdir,
-                monochrome_logs,
-                multiqc_report.toList()
+                monochrome_logs
             )
         }