From 88d742348fed0f1e13e217ecf562d3711937a8fa Mon Sep 17 00:00:00 2001 From: DLBPointon Date: Tue, 26 Nov 2024 14:41:37 +0000 Subject: [PATCH] Pre Commit linting --- assets/github_testing/github_test.yaml | 2 +- modules.json | 98 +++++-------------- .../custom/getchromsizes/environment.yml | 6 +- 3 files changed, 29 insertions(+), 77 deletions(-) diff --git a/assets/github_testing/github_test.yaml b/assets/github_testing/github_test.yaml index 3bdad325..0ec46055 100644 --- a/assets/github_testing/github_test.yaml +++ b/assets/github_testing/github_test.yaml @@ -23,4 +23,4 @@ vecscreen_database_path: /home/runner/work/ascc/ascc/vecscreen/ seqkit_sliding: 100000 seqkit_window: 6000 n_neighbours: 13 -btk_yaml: /home/runner/work/ascc/ascc/assets/btk_draft.yaml \ No newline at end of file +btk_yaml: /home/runner/work/ascc/ascc/assets/btk_draft.yaml diff --git a/modules.json b/modules.json index 4feb539d..c399d570 100644 --- a/modules.json +++ b/modules.json @@ -8,151 +8,109 @@ "blast/blastn": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "blast/makeblastdb": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/blast/makeblastdb/blast-makeblastdb.diff" }, "custom/getchromsizes": { "branch": "master", "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/custom/getchromsizes/custom-getchromsizes.diff" }, "diamond/blastx": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "fastqc": { "branch": "master", "git_sha": "21f230b8cca43755bf73470e6fd0290832a98aef", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "fcs/fcsadaptor": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "fcs/fcsgx": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gnu/sort": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "kraken2/kraken2": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "minimap2/align": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "minimap2/index": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "multiqc": { "branch": "master", "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "ncbitools/vecscreen": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/depth": { "branch": "master", "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/faidx": { "branch": "master", "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/index": { "branch": "master", "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/merge": { "branch": "master", "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/sort": { "branch": "master", "git_sha": "b7800db9b069ed505db3f9d91b8c72faea9be17b", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/view": { "branch": "master", "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "seqkit/sliding": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "tiara/tiara": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] } } }, @@ -161,26 +119,20 @@ "utils_nextflow_pipeline": { "branch": "master", "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "utils_nfvalidation_plugin": { "branch": "master", "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] } } } } } -} \ No newline at end of file +} diff --git a/modules/nf-core/custom/getchromsizes/environment.yml b/modules/nf-core/custom/getchromsizes/environment.yml index 45639dce..78d4c184 100644 --- a/modules/nf-core/custom/getchromsizes/environment.yml +++ b/modules/nf-core/custom/getchromsizes/environment.yml @@ -1,5 +1,5 @@ channels: - - conda-forge - - bioconda + - conda-forge + - bioconda dependencies: - - bioconda::samtools=1.16.1 + - bioconda::samtools=1.16.1