diff --git a/subworkflows/local/starsolo.nf b/subworkflows/local/starsolo.nf index 642252d..dad91aa 100644 --- a/subworkflows/local/starsolo.nf +++ b/subworkflows/local/starsolo.nf @@ -10,7 +10,11 @@ workflow STARSOLO { ch_versions = Channel.empty() - STARSOLO_ALIGN ( reads, index ) + STARSOLO_ALIGN ( + reads, + Channel.fromPath("$projectDir/assets/whitelist.tsv", checkIfExists: true), + index + ) ch_versions = ch_versions.mix(STARSOLO_ALIGN.out.versions.first()) diff --git a/workflows/primeseq.nf b/workflows/primeseq.nf index 4575560..4cc24d6 100644 --- a/workflows/primeseq.nf +++ b/workflows/primeseq.nf @@ -48,7 +48,6 @@ workflow PRIMESEQ { [ id: meta.id, plate_id: meta.plate_id, - whitelist: , umi_len: 16, umi_start: 13, cb_len: 12, @@ -56,11 +55,7 @@ workflow PRIMESEQ { ], "CB_UMI_Simple", fastq ] } - STARSOLO ( - ch_reads, - file("$projectDir/assets/whitelist.tsv", checkIfExists: true), - ch_star_index - ) + STARSOLO ( ch_reads, ch_star_index ) ch_versions = ch_versions.mix(STARSOLO.out.versions.first()) ch_multiqc_files = ch_multiqc_files.mix(STARSOLO.out.for_multiqc) @@ -117,7 +112,9 @@ workflow PRIMESEQ { ch_multiqc_files.collect(), ch_multiqc_config.toList(), ch_multiqc_custom_config.toList(), - ch_multiqc_logo.toList() + ch_multiqc_logo.toList(), + false, + false ) emit: