From 03c7fba5900b4ec14d0a9888a39f4c6db8847673 Mon Sep 17 00:00:00 2001 From: "J. Sebastian Paez" Date: Mon, 23 Oct 2023 12:26:16 -0700 Subject: [PATCH 1/3] added node packages to gitignore --- .gitignore | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/.gitignore b/.gitignore index 534477da..401d816d 100644 --- a/.gitignore +++ b/.gitignore @@ -12,3 +12,8 @@ testing* /build/ results*/ venv/ +node_modules +conversion_inputs +debug_dir +test_out + From 00e05d29902ec7b6bc8d925c176959ce0e4d9c63 Mon Sep 17 00:00:00 2001 From: "J. Sebastian Paez" Date: Mon, 23 Oct 2023 12:33:22 -0700 Subject: [PATCH 2/3] updated decompression --- modules/local/decompress_dotd/main.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/local/decompress_dotd/main.nf b/modules/local/decompress_dotd/main.nf index f8136c0b..e345300f 100644 --- a/modules/local/decompress_dotd/main.nf +++ b/modules/local/decompress_dotd/main.nf @@ -59,7 +59,7 @@ process DECOMPRESS { tar --help 2>&1 | tee -a ${prefix}_decompression.log gunzip --help 2>&1 | tee -a ${prefix}_decompression.log - zip --help 2>&1 | tee -a ${prefix}_decompression.log + (unzip --help 2>&1 || zip --help 2>&1) | tee -a ${prefix}_decompression.log echo "Unpacking..." | tee -a ${compressed_file.baseName}_decompression.log extract ${compressed_file} 2>&1 | tee -a ${compressed_file.baseName}_conversion.log @@ -73,7 +73,7 @@ process DECOMPRESS { "${task.process}": gunzip: \$(gunzip --help 2>&1 | head -1 | grep -oE "\\d+\\.\\d+(\\.\\d+)?") tar: \$(tar --help 2>&1 | head -1 | grep -oE "\\d+\\.\\d+(\\.\\d+)?") - zip: \$(zip --help | head -2 | tail -1 | grep -oE "\\d+\\.\\d+") + zip: \$((unzip --help 2>&1 || zip --help 2>&1) | head -2 | tail -1 | grep -oE "\\d+\\.\\d+") END_VERSIONS """ } From 28f7d5d0f838c1bdf53fb935a07cfc92e62db7d3 Mon Sep 17 00:00:00 2001 From: "J. Sebastian Paez" Date: Mon, 23 Oct 2023 14:32:33 -0700 Subject: [PATCH 3/3] changed container for dotd2mqc --- modules/local/dotd_to_mqc/main.nf | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/modules/local/dotd_to_mqc/main.nf b/modules/local/dotd_to_mqc/main.nf index cdf080f7..60b08b9f 100644 --- a/modules/local/dotd_to_mqc/main.nf +++ b/modules/local/dotd_to_mqc/main.nf @@ -44,7 +44,11 @@ process DOTD2MQC_AGGREGATE { label 'process_single' conda 'base::python=3.10' - container 'continuumio/miniconda3:23.5.2-0-alpine' + if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { + container "https://depot.galaxyproject.org/singularity/python:3.10" + } else { + container "quay.io/biocontainers/python:3.10" + } input: path '*' // tsv files from DOTD2MQC_INDIVIDUAL