Commit 5d167018 authored by Chris Cheshire's avatar Chris Cheshire
Browse files

Module update fixes for pipeline

parent fb4f3fbd

conf/modules.config

+2 −2
Original line number Original line Diff line number Diff line
@@ -334,7 +334,7 @@ if(params.run_q_filter) { 
if(params.run_mark_dups) {

if(params.run_mark_dups) {

    process {

    process {

        withName: 'NFCORE_CUTANDRUN:CUTANDRUN:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES' {

        withName: 'NFCORE_CUTANDRUN:CUTANDRUN:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES' {

            ext.args = "ASSUME_SORT_ORDER=coordinate REMOVE_DUPLICATES=false VALIDATION_STRINGENCY=LENIENT TMP_DIR=tmp"

            ext.args = "--ASSUME_SORT_ORDER coordinate --REMOVE_DUPLICATES false --VALIDATION_STRINGENCY LENIENT --TMP_DIR tmp"

            ext.prefix = { "${meta.id}.target.markdup" }

            ext.prefix = { "${meta.id}.target.markdup" }

            publishDir = [

            publishDir = [

                path: { "${params.outdir}/02_alignment/${params.aligner}/target" },

                path: { "${params.outdir}/02_alignment/${params.aligner}/target" },
@@ -367,7 +367,7 @@ if(params.run_mark_dups) { 
if(params.run_remove_dups) {

if(params.run_remove_dups) {

    process {

    process {

        withName: 'NFCORE_CUTANDRUN:CUTANDRUN:DEDUPLICATE_PICARD:PICARD_MARKDUPLICATES' {

        withName: 'NFCORE_CUTANDRUN:CUTANDRUN:DEDUPLICATE_PICARD:PICARD_MARKDUPLICATES' {

            ext.args = "ASSUME_SORT_ORDER=coordinate REMOVE_DUPLICATES=false VALIDATION_STRINGENCY=LENIENT TMP_DIR=tmp"

            ext.args = "--ASSUME_SORT_ORDER coordinate --REMOVE_DUPLICATES false --VALIDATION_STRINGENCY LENIENT --TMP_DIR tmp"

            ext.prefix = { "${meta.id}.target.dedup" }

            ext.prefix = { "${meta.id}.target.dedup" }

            publishDir = [

            publishDir = [

                path: { "${params.outdir}/02_alignment/${params.aligner}/target" },

                path: { "${params.outdir}/02_alignment/${params.aligner}/target" },

subworkflows/local/calculate_fragments.nf

+1 −1
Original line number Original line Diff line number Diff line
@@ -18,7 +18,7 @@ workflow CALCULATE_FRAGMENTS { 
    /*

    /*

     * Filter BAM file

     * Filter BAM file

     */

     */

    SAMTOOLS_VIEW ( bam, [] )

    SAMTOOLS_VIEW ( bam.map{ row -> [ row[0], row[1], [] ] }, [] )

    ch_versions = ch_versions.mix(SAMTOOLS_VIEW.out.versions)

    ch_versions = ch_versions.mix(SAMTOOLS_VIEW.out.versions)





    /*

    /*

subworkflows/local/prepare_genome.nf

+2 −2
Original line number Original line Diff line number Diff line
@@ -84,7 +84,7 @@ workflow PREPARE_GENOME { 
    if ("bowtie2" in prepare_tool_indices) {

    if ("bowtie2" in prepare_tool_indices) {

        if (params.bowtie2) {

        if (params.bowtie2) {

            if (params.bowtie2.endsWith(".tar.gz")) {

            if (params.bowtie2.endsWith(".tar.gz")) {

                ch_bt2_index = UNTAR_INDEX_TARGET ( params.bowtie2 ).untar

                ch_bt2_index = UNTAR_INDEX_TARGET ( [ [], params.bowtie2 ] ).untar.map{ row -> [ row[1] ] }

                ch_versions  = ch_versions.mix(UNTAR_INDEX_TARGET.out.versions)

                ch_versions  = ch_versions.mix(UNTAR_INDEX_TARGET.out.versions)

            } else {

            } else {

                ch_bt2_index = file(params.bowtie2)

                ch_bt2_index = file(params.bowtie2)
@@ -96,7 +96,7 @@ workflow PREPARE_GENOME { 




        if (params.spikein_bowtie2) {

        if (params.spikein_bowtie2) {

            if (params.spikein_bowtie2.endsWith(".tar.gz")) {

            if (params.spikein_bowtie2.endsWith(".tar.gz")) {

                ch_bt2_spikein_index = UNTAR_INDEX_SPIKEIN ( params.spikein_bowtie2 ).untar

                ch_bt2_spikein_index = UNTAR_INDEX_SPIKEIN ( [ [], params.spikein_bowtie2 ] ).untar.map{ row -> [ row[1] ] }

                ch_versions          = ch_versions.mix(UNTAR_INDEX_SPIKEIN.out.versions)

                ch_versions          = ch_versions.mix(UNTAR_INDEX_SPIKEIN.out.versions)

            } else {

            } else {

                ch_bt2_spikein_index = file(params.spikein_bowtie2)

                ch_bt2_spikein_index = file(params.spikein_bowtie2)

subworkflows/nf-core/samtools_view_sort_stats.nf

+1 −1
Original line number Original line Diff line number Diff line
@@ -16,7 +16,7 @@ workflow SAMTOOLS_VIEW_SORT_STATS { 
    /*

    /*

     * Filter BAM file

     * Filter BAM file

     */

     */

    SAMTOOLS_VIEW ( bam, [] )

    SAMTOOLS_VIEW ( bam.map{ row -> [ row[0], row[1], [] ] }, [] )

    ch_versions = ch_versions.mix(SAMTOOLS_VIEW.out.versions.first())

    ch_versions = ch_versions.mix(SAMTOOLS_VIEW.out.versions.first())





    /*

    /*

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