improve code formatting

nf-core · Oct 29, 2024 · dff4907 · dff4907
1 parent 55e5a02
commit dff4907
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Showing 5 changed files with 138 additions and 138 deletions.
diff --git a/modules/local/bbmaprepair/main.nf b/modules/local/bbmaprepair/main.nf
@@ -17,33 +17,33 @@ process BBMAPREPAIR {
         task.ext.when == null || task.ext.when
 
     script:
-        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> ${fastq[0].baseName}_repair.log
-
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            repair.sh: \$(bbversion.sh)
-        END_VERSIONS
+    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> ${fastq[0].baseName}_repair.log
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        repair.sh: \$(bbversion.sh)
+    END_VERSIONS
     """
 
     stub:
-        def infastq1 = fastq[0]
-        def infastq2 = fastq[1]
-        def outfastq1 = infastq1.baseName
-        def outfastq2 = infastq2.baseName
-        """
-        touch ${outfastq1}_interleaving.fastq.gz
-        touch ${outfastq2}_interleaving.fastq.gz
-        touch ${fastq[0].baseName}_singletons.fastq.gz
-        touch ${fastq[0].baseName}_repair.log
-
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            repair.sh: \$(bbversion.sh)
-        END_VERSIONS
+    def infastq1 = fastq[0]
+    def infastq2 = fastq[1]
+    def outfastq1 = infastq1.baseName
+    def outfastq2 = infastq2.baseName
+    """
+    touch ${outfastq1}_interleaving.fastq.gz
+    touch ${outfastq2}_interleaving.fastq.gz
+    touch ${fastq[0].baseName}_singletons.fastq.gz
+    touch ${fastq[0].baseName}_repair.log
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        repair.sh: \$(bbversion.sh)
+    END_VERSIONS
     """
 }
diff --git a/modules/local/renamer/main.nf b/modules/local/renamer/main.nf
@@ -15,59 +15,59 @@ process RENAMER {
     task.ext.when == null || task.ext.when
 
     script:
-        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 VERSION = '1.0.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
 
-        def rep1 = report[0]
-        def rep2 = report[1]
-        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()
+    def fq1 = fastq[0]
+    def fq2 = fastq[1]
 
-        """
-        # Rename FASTQ files
-        if [[ ${is_single_end_fq} = true ]]; then
-            # No second file, treat as single-end
-            cp ${fq1} ${new_name_fqsingle}
-        elif [[ "${fq1}" == *"trim_2.fastq_interleaving.fastq.gz" ]]; then
-            new_name_fq1="${meta_fastq.id}_R2_repaired.fastq.gz"
-            new_name_fq2="${meta_fastq.id}_R1_repaired.fastq.gz"
-            cp "${fq1}" "${new_name_fq1}"
-            cp "${fq2}" "${new_name_fq2}"
-        elif [[ "${fq1}" == *"trim_1.fastq_interleaving.fastq.gz" ]]; then
-            new_name_fq2="${meta_fastq.id}_R2_repaired.fastq.gz"
-            new_name_fq1="${meta_fastq.id}_R1_repaired.fastq.gz"
-            cp "${fq1}" "${new_name_fq1}"
-            cp "${fq2}" "${new_name_fq2}"
-        fi
+    def new_name_fq1 = "${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()
 
-        # Rename REPORT files
-        if [[ ${is_single_end_report} = true ]]; then
-            cp ${rep1} ${new_name_repsingle}
-        elif [[ "${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"
-            cp "${rep1}" "${new_name_rep1}"
-            cp "${rep2}" "${new_name_rep2}"
-        elif [[ "${rep1}" == *"R1.fastq_recovered_merged_report.txt" ]]; then
-            new_name_rep2="${meta_report.id}_R2_report.txt"
-            new_name_rep1="${meta_report.id}_R1_report.txt"
-            cp "${rep1}" "${new_name_rep1}"
-            cp "${rep2}" "${new_name_rep2}"
-        fi
+    def rep1 = report[0]
+    def rep2 = report[1]
+    def new_name_rep1 = "${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()
 
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-        renamer: $VERSION
-        END_VERSIONS
+    """
+    # Rename FASTQ files
+    if [[ ${is_single_end_fq} = true ]]; then
+        # No second file, treat as single-end
+        cp ${fq1} ${new_name_fqsingle}
+    elif [[ "${fq1}" == *"trim_2.fastq_interleaving.fastq.gz" ]]; then
+        new_name_fq1="${meta_fastq.id}_R2_repaired.fastq.gz"
+        new_name_fq2="${meta_fastq.id}_R1_repaired.fastq.gz"
+        cp "${fq1}" "${new_name_fq1}"
+        cp "${fq2}" "${new_name_fq2}"
+    elif [[ "${fq1}" == *"trim_1.fastq_interleaving.fastq.gz" ]]; then
+        new_name_fq2="${meta_fastq.id}_R2_repaired.fastq.gz"
+        new_name_fq1="${meta_fastq.id}_R1_repaired.fastq.gz"
+        cp "${fq1}" "${new_name_fq1}"
+        cp "${fq2}" "${new_name_fq2}"
+    fi
+
+    # Rename REPORT files
+    if [[ ${is_single_end_report} = true ]]; then
+        cp ${rep1} ${new_name_repsingle}
+    elif [[ "${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"
+        cp "${rep1}" "${new_name_rep1}"
+        cp "${rep2}" "${new_name_rep2}"
+    elif [[ "${rep1}" == *"R1.fastq_recovered_merged_report.txt" ]]; then
+        new_name_rep2="${meta_report.id}_R2_report.txt"
+        new_name_rep1="${meta_report.id}_R1_report.txt"
+        cp "${rep1}" "${new_name_rep1}"
+        cp "${rep2}" "${new_name_rep2}"
+    fi
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+    renamer: $VERSION
+    END_VERSIONS
     """
 
     stub:

diff --git a/modules/local/wipertools/gather.nf b/modules/local/wipertools/gather.nf
@@ -16,28 +16,28 @@ process GATHER {
     task.ext.when == null || task.ext.when
 
     script:
-        def VERSION = '1.0.1' // 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 ${fastq_list} > ${filename}_merged_wiped.fastq.gz
+    wipertools summarygather -s ${report_list} -f ${filename}_merged_report.txt
 
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
         wipertools: $VERSION
-        END_VERSIONS
-        """
+    END_VERSIONS
+    """
 
     stub:
-        def VERSION = '1.0.1' // 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
+    """
+    gzip < /dev/null > ${filename}_merged_wiped.fastq.gz
+    touch ${filename}_merged_report.txt
 
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
         wipertools: $VERSION
-        END_VERSIONS
-        """
+    END_VERSIONS
+    """
 }
diff --git a/modules/local/wipertools/scatter.nf b/modules/local/wipertools/scatter.nf
@@ -10,33 +10,33 @@ process SCATTER {
     path "versions.yml"                     , emit: versions
 
     script:
-        def args = task.ext.args ?: ''
-        def prefix = task.ext.prefix ?: "${meta.id}"
-        def filename = "${fastq.baseName}"
-        def VERSION = '1.0.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def filename = "${fastq.baseName}"
+    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.
+    """
+    split -a3 -l ${params.chunk_size} --numeric-suffixes=1 --additional-suffix .fastq ${fastq} ${filename}_chunk.
 
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            wipertools: $VERSION
-        END_VERSIONS
-        """
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        wipertools: $VERSION
+    END_VERSIONS
+    """
 
     stub:
-        def args = task.ext.args ?: ''
-        def prefix = task.ext.prefix ?: "${meta.id}"
-        def filename = "${fastq.baseName}"
-        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
-        touch ${filename}_chunk.002.fastq
-
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            wipertools: $VERSION
-        END_VERSIONS
-        """
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def filename = "${fastq.baseName}"
+    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
+    touch ${filename}_chunk.002.fastq
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        wipertools: $VERSION
+    END_VERSIONS
+    """
 }
diff --git a/modules/local/wipertools/wipe.nf b/modules/local/wipertools/wipe.nf
@@ -15,32 +15,32 @@ process WIPER {
         task.ext.when == null || task.ext.when
 
     script:
-        def args = task.ext.args ?: ''
-        def filename = "${fastq.baseName}"
-        def VERSION = '1.0.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
-        def log_freq = (params.chunk_size / 100 as Integer) * 10
-        log_freq = log_freq == 0 ? 1 : log_freq
+    def args = task.ext.args ?: ''
+    def filename = "${fastq.baseName}"
+    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
 
-        """
-        wipertools fastqwiper -i $fastq -o ${filename}_wiped.fastq.gz -f ${log_freq} -a ${params.alphabet} -l ${filename}_report.txt
+    """
+    wipertools fastqwiper -i $fastq -o ${filename}_wiped.fastq.gz -f ${log_freq} -a ${params.alphabet} -l ${filename}_report.txt
 
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            wipertools: $VERSION
-        END_VERSIONS
-        """
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        wipertools: $VERSION
+    END_VERSIONS
+    """
 
     stub:
-        def args = task.ext.args ?: ''
-        def filename = "${fastq.baseName}"
-        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 ${filename}_report.txt
-
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            wipertools: $VERSION
-        END_VERSIONS
+    def args = task.ext.args ?: ''
+    def filename = "${fastq.baseName}"
+    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 ${filename}_report.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        wipertools: $VERSION
+    END_VERSIONS
     """
 }