From 3ad796ff90628e4678b6890e5898cc31fb0b53c9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E2=80=98ens-ftricomi=E2=80=99?= Date: Tue, 3 Sep 2024 16:42:03 +0100 Subject: [PATCH] cleaning --- .../modules/process_taxonomy_info/get_run_accessions.nf | 7 ++----- .../modules/transcriptomic_alignment/index_genome.nf | 4 ++-- 2 files changed, 4 insertions(+), 7 deletions(-) diff --git a/pipelines/nextflow/modules/process_taxonomy_info/get_run_accessions.nf b/pipelines/nextflow/modules/process_taxonomy_info/get_run_accessions.nf index 14b3a1c..cb5e2b8 100644 --- a/pipelines/nextflow/modules/process_taxonomy_info/get_run_accessions.nf +++ b/pipelines/nextflow/modules/process_taxonomy_info/get_run_accessions.nf @@ -41,14 +41,13 @@ process GET_RUN_ACCESSIONS { path("run_accession_list.txt") script: - //def runAccessionBatch = run_accession_batch ? run_accession_batch : null - runAccessionList = [] + runAccessionList = [] runAccessionToFile='run_accession_list.txt' def fileBatch=new File(run_accession_batch) if (fileBatch.exists()){ fileBatch.eachLine { line -> runAccessionList.add([taxon_id: taxon_id, gca: gca, run_accession: line]) -} + } """ cat ${run_accession_batch.toString()} > $runAccessionToFile """ @@ -89,8 +88,6 @@ process GET_RUN_ACCESSIONS { } reader.close() -// runAccessionToFile='run_accession_list.txt' - //cp $run_accession_batch $runAccessionToFile log.info("BATCH FILE ${run_accession_batch}") """ echo '${responseContent.toString()}' > $runAccessionToFile diff --git a/pipelines/nextflow/modules/transcriptomic_alignment/index_genome.nf b/pipelines/nextflow/modules/transcriptomic_alignment/index_genome.nf index 8b6c898..6f57490 100644 --- a/pipelines/nextflow/modules/transcriptomic_alignment/index_genome.nf +++ b/pipelines/nextflow/modules/transcriptomic_alignment/index_genome.nf @@ -70,8 +70,8 @@ process INDEX_GENOME { // Calculate the genome length (excluding header lines) //def genomeLength = fastaContent.split('\n').findAll { !it.startsWith('>') }.join('').length() - if (genomeLength != 0) { - filesValid = true + if (genomeLength != 0) { + filesValid = true } } // Define read length (you may need to adjust this based on your data)