From b8a2a07ee3224233c6575367641ddc8c8097a035 Mon Sep 17 00:00:00 2001 From: edsu7 <22638361+edsu7@users.noreply.github.com> Date: Tue, 16 Aug 2022 16:58:23 -0400 Subject: [PATCH 1/2] [wfpm v0.8.0] started a new version ega-download-wf@0.1.1 from ega-download-wf@0.1.0 which was in development --- ega-download-wf/main.nf | 2 +- ega-download-wf/pkg.json | 2 +- ega-download-wf/tests/checker.nf | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/ega-download-wf/main.nf b/ega-download-wf/main.nf index ade5867..1e97627 100755 --- a/ega-download-wf/main.nf +++ b/ega-download-wf/main.nf @@ -21,7 +21,7 @@ */ nextflow.enable.dsl = 2 -version = '0.1.0' // package version +version = '0.1.1' // universal params go here, change default value as needed params.container = "" diff --git a/ega-download-wf/pkg.json b/ega-download-wf/pkg.json index 125f82a..a7b2c88 100644 --- a/ega-download-wf/pkg.json +++ b/ega-download-wf/pkg.json @@ -1,6 +1,6 @@ { "name": "ega-download-wf", - "version": "0.1.0", + "version": "0.1.1", "description": "Workflow wrapper for various methods to download data from EGA-archive", "main": "main.nf", "deprecated": false, diff --git a/ega-download-wf/tests/checker.nf b/ega-download-wf/tests/checker.nf index 284a7ac..586fd1a 100755 --- a/ega-download-wf/tests/checker.nf +++ b/ega-download-wf/tests/checker.nf @@ -26,7 +26,7 @@ */ nextflow.enable.dsl = 2 -version = '0.1.0' // package version +version = '0.1.1' // universal params params.publish_dir = "" From 5e3ec208f89a2ed46f2d4ba113f46d2632b9c68b Mon Sep 17 00:00:00 2001 From: edsu7 <22638361+edsu7@users.noreply.github.com> Date: Wed, 17 Aug 2022 08:08:58 -0400 Subject: [PATCH 2/2] temporarily removing sanity checks --- ega-download-wf/main.nf | 40 ++++--------------- ega-download-wf/tests/input/pyega3.tsv | 2 + ...aspera.json => local-test-job-aspera.json} | 3 +- ...b-pyega.json => local-test-job-pyega.json} | 2 +- 4 files changed, 12 insertions(+), 35 deletions(-) create mode 100644 ega-download-wf/tests/input/pyega3.tsv rename ega-download-wf/tests/{test-job-aspera.json => local-test-job-aspera.json} (68%) rename ega-download-wf/tests/{test-job-pyega.json => local-test-job-pyega.json} (80%) diff --git a/ega-download-wf/main.nf b/ega-download-wf/main.nf index 1e97627..96f2b9f 100755 --- a/ega-download-wf/main.nf +++ b/ega-download-wf/main.nf @@ -36,14 +36,13 @@ params.input_file = "" params.cleanup = true params.download_mode="" -params.files_to_download=[] -params.ids_to_download=[] +params.file_info_tsv="NO_FILE1" params.ascp_scp_host="" params.ascp_scp_user="" params.aspera_scp_pass="" -params.c4gh_secret_key="NO_FILE" +params.c4gh_secret_key="NO_FILE2" params.c4gh_pass_phrase="" params.pyega3_ega_user="" @@ -53,15 +52,11 @@ include { downloadPyega3 } from './wfpr_modules/github.com/icgc-argo/argo-data-s include { downloadAspera } from './wfpr_modules/github.com/icgc-argo/argo-data-submission/download-aspera@0.1.0/main.nf' params([*:params, 'cleanup': false]) include { decryptAspera } from './wfpr_modules/github.com/icgc-argo/argo-data-submission/decrypt-aspera@0.1.0/main.nf' params([*:params, 'cleanup': false]) -Channel.fromList(params.files_to_download).set{file_ch} -Channel.fromList(params.ids_to_download).set{id_ch} - // please update workflow code as needed workflow EgaDownloadWf { take: // update as needed download_mode - files_to_download - ids_to_download + file_info_tsv ascp_scp_host ascp_scp_user aspera_scp_pass @@ -70,24 +65,13 @@ workflow EgaDownloadWf { c4gh_secret_key c4gh_pass_phrase main: // update as needed - + Channel.fromPath(file_info_tsv).splitCsv(sep:'\t',header:true).map( row -> row.path).set{file_ch} + Channel.fromPath(file_info_tsv).splitCsv(sep:'\t',header:true).map( row -> row.ega_file_id).set{id_ch} if ( download_mode=='aspera' ){ - if (id_ch.count()!=file_ch.count()){ - println "# of ega_file_ids != # of file paths. Please Correct." - exit 1 - } - else if (files_to_download.size()==0){ - println "# of ega_file_ids != # of file paths. Please Correct." - exit 1 - } - else if (ids_to_download.size()==0){ - println "# of ega_file_ids != # of file paths. Please Correct." - exit 1 - } else { downloadAspera( - files_to_download, - ids_to_download, + file_ch, + id_ch, ascp_scp_host, ascp_scp_user, aspera_scp_pass) @@ -99,14 +83,7 @@ workflow EgaDownloadWf { ) sequence_files=decryptAspera.out.output_files.collect() - } } else if (download_mode=='pyega3'){ - - if (ids_to_download.size()==0){ - println "# of ega_file_ids must be greater than 0. Please Correct." - exit 1 - } - downloadPyega3( id_ch, pyega3_ega_user, @@ -131,8 +108,7 @@ workflow EgaDownloadWf { workflow { EgaDownloadWf( params.download_mode, - params.files_to_download, - params.ids_to_download, + params.file_info_tsv, params.ascp_scp_host, params.ascp_scp_user, params.aspera_scp_pass, diff --git a/ega-download-wf/tests/input/pyega3.tsv b/ega-download-wf/tests/input/pyega3.tsv new file mode 100644 index 0000000..861925a --- /dev/null +++ b/ega-download-wf/tests/input/pyega3.tsv @@ -0,0 +1,2 @@ +ega_file_id path +EGAF00001770106 EGAF00001770106.bam diff --git a/ega-download-wf/tests/test-job-aspera.json b/ega-download-wf/tests/local-test-job-aspera.json similarity index 68% rename from ega-download-wf/tests/test-job-aspera.json rename to ega-download-wf/tests/local-test-job-aspera.json index 2baa003..47606e9 100644 --- a/ega-download-wf/tests/test-job-aspera.json +++ b/ega-download-wf/tests/local-test-job-aspera.json @@ -1,6 +1,5 @@ { - "ids_to_download," : "EGAF00001770106", - "files_to_download," : "EGAF00001770106.bam", + "file_info_tsv" : "tests/input/pyega3.tsv", "pyega3_ega_user" : "ega-test-data@ebi.ac.uk", "pyega3_ega_pass" : "egarocks", "download_mode" : "aspera", diff --git a/ega-download-wf/tests/test-job-pyega.json b/ega-download-wf/tests/local-test-job-pyega.json similarity index 80% rename from ega-download-wf/tests/test-job-pyega.json rename to ega-download-wf/tests/local-test-job-pyega.json index c301743..165e283 100644 --- a/ega-download-wf/tests/test-job-pyega.json +++ b/ega-download-wf/tests/local-test-job-pyega.json @@ -1,5 +1,5 @@ { - "ids_to_download" : ["EGAF00001770106"], + "file_info_tsv" : "tests/input/pyega3.tsv", "pyega3_ega_user" : "ega-test-data@ebi.ac.uk", "pyega3_ega_pass" : "egarocks", "download_mode" : "pyega3",