From 8b701b0174d4b6d69d003f9bc35ad5b222b19e5c Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Fri, 29 Sep 2023 11:03:25 +0200 Subject: [PATCH 1/4] Fix "Argument list too long" issue --- modules/local/download_pdbmmcif.nf | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/modules/local/download_pdbmmcif.nf b/modules/local/download_pdbmmcif.nf index 0502175a..61e2977f 100644 --- a/modules/local/download_pdbmmcif.nf +++ b/modules/local/download_pdbmmcif.nf @@ -41,7 +41,9 @@ process DOWNLOAD_PDBMMCIF { raw echo "Unzipping all mmCIF files..." - find ./raw -type f -name '*.[gG][zZ]' -exec gunzip {} + + find ./raw -type f -name '*.[gG][zZ]' -print0 | while IFS= read -r -d $'\0' file; do + gunzip "$file" + done echo "Flattening all mmCIF files..." mkdir mmcif_files From a9ef4a88b003cf49d40acbb23d3b2f359edcced4 Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Fri, 29 Sep 2023 11:13:53 +0200 Subject: [PATCH 2/4] Fix changelog msg --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3d1fd181..c8552942 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -19,7 +19,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [PR #100](https://github.com/nf-core/proteinfold/pull/100) - Update containers for AlphaFold2 and ColabFold local modules. - [PR #105](https://github.com/nf-core/proteinfold/pull/105) - Update COLABFOLD_BATCH docker container, metro map figure and nextflow schema description. - [PR #106](https://github.com/nf-core/proteinfold/pull/106) - Add `singularity.registry = 'quay.io'` and bump NF version to 23.04.0 -- [PR #108](https://github.com/nf-core/proteinfold/pull/108) - Fix gunzip error when providing too many files when downloading PDBMMCIF database. +- [[#108](https://github.com/nf-core/proteinfold/issues/108)] - Fix gunzip error when providing too many files when downloading PDBMMCIF database. - [PR #111](https://github.com/nf-core/proteinfold/pull/111) - Update pipeline template to [nf-core/tools 2.9](https://github.com/nf-core/tools/releases/tag/2.9). - [PR #112](https://github.com/nf-core/rnaseq/pull/112) - Use `nf-validation` plugin for parameter and samplesheet validation. - [#113](https://github.com/nf-core/proteinfold/pull/113) - Include esmfold dbs for full data sets. From 59d43d9e36fb4d98d9004bcff9a95eeb9347aff3 Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Fri, 29 Sep 2023 11:17:09 +0200 Subject: [PATCH 3/4] Format changelog --- CHANGELOG.md | 30 +++++++++++++++--------------- 1 file changed, 15 insertions(+), 15 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index c8552942..175fbef6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,24 +7,24 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Enhancements & fixes -- [#80](https://github.com/nf-core/proteinfold/pull/80) - Add `accelerator` directive to GPU processes when `params.use_gpu` is true. -- [#81](https://github.com/nf-core/proteinfold/pull/81) - Support multiline fasta for colabfold multimer predictions. -- [#89](https://github.com/nf-core/proteinfold/pull/89) - Fix issue with excessive symlinking in the pdb_mmcif database. -- [PR #91](https://github.com/nf-core/proteinfold/pull/91) - Update ColabFold version to 1.5.2 and AlphaFold version to 2.3.2 -- [PR #92](https://github.com/nf-core/proteinfold/pull/92) - Add ESMFold workflow to the pipeline. +- [[#80](https://github.com/nf-core/proteinfold/pull/80)] - Add `accelerator` directive to GPU processes when `params.use_gpu` is true. +- [[#81](https://github.com/nf-core/proteinfold/pull/81)] - Support multiline fasta for colabfold multimer predictions. +- [[#89](https://github.com/nf-core/proteinfold/pull/89)] - Fix issue with excessive symlinking in the pdb_mmcif database. +- [[PR #91](https://github.com/nf-core/proteinfold/pull/91)] - Update ColabFold version to 1.5.2 and AlphaFold version to 2.3.2 +- [[PR #92](https://github.com/nf-core/proteinfold/pull/92)] - Add ESMFold workflow to the pipeline. - Update metro map to include ESMFold workflow. - Update modules to remove quay from container url. -- [nf-core/tools#2286](https://github.com/nf-core/tools/issues/2286) - Set default container registry outside profile scope. -- [PR #97](https://github.com/nf-core/proteinfold/pull/97) - Fix issue with uniref30 missing path when using the full BFD database in AlphaFold. -- [PR #100](https://github.com/nf-core/proteinfold/pull/100) - Update containers for AlphaFold2 and ColabFold local modules. -- [PR #105](https://github.com/nf-core/proteinfold/pull/105) - Update COLABFOLD_BATCH docker container, metro map figure and nextflow schema description. -- [PR #106](https://github.com/nf-core/proteinfold/pull/106) - Add `singularity.registry = 'quay.io'` and bump NF version to 23.04.0 +- [[nf-core/tools#2286](https://github.com/nf-core/tools/issues/2286)] - Set default container registry outside profile scope. +- [[PR #97](https://github.com/nf-core/proteinfold/pull/97)] - Fix issue with uniref30 missing path when using the full BFD database in AlphaFold. +- [[PR #100](https://github.com/nf-core/proteinfold/pull/100)] - Update containers for AlphaFold2 and ColabFold local modules. +- [[PR #105](https://github.com/nf-core/proteinfold/pull/105)] - Update COLABFOLD_BATCH docker container, metro map figure and nextflow schema description. +- [[PR #106](https://github.com/nf-core/proteinfold/pull/106)] - Add `singularity.registry = 'quay.io'` and bump NF version to 23.04.0 - [[#108](https://github.com/nf-core/proteinfold/issues/108)] - Fix gunzip error when providing too many files when downloading PDBMMCIF database. -- [PR #111](https://github.com/nf-core/proteinfold/pull/111) - Update pipeline template to [nf-core/tools 2.9](https://github.com/nf-core/tools/releases/tag/2.9). -- [PR #112](https://github.com/nf-core/rnaseq/pull/112) - Use `nf-validation` plugin for parameter and samplesheet validation. -- [#113](https://github.com/nf-core/proteinfold/pull/113) - Include esmfold dbs for full data sets. -- [PR #114](https://github.com/nf-core/rnaseq/pull/114) - Update paths to test dbs. -- [PR #117](https://github.com/nf-core/proteinfold/pull/117) - Update pipeline template to [nf-core/tools 2.10](https://github.com/nf-core/tools/releases/tag/2.10). +- [[PR #111](https://github.com/nf-core/proteinfold/pull/111)] - Update pipeline template to [nf-core/tools 2.9](https://github.com/nf-core/tools/releases/tag/2.9). +- [[PR #112](https://github.com/nf-core/rnaseq/pull/112)] - Use `nf-validation` plugin for parameter and samplesheet validation. +- [[#113](https://github.com/nf-core/proteinfold/pull/113)] - Include esmfold dbs for full data sets. +- [[PR #114](https://github.com/nf-core/rnaseq/pull/114)] - Update paths to test dbs. +- [[PR #117](https://github.com/nf-core/proteinfold/pull/117)] - Update pipeline template to [nf-core/tools 2.10](https://github.com/nf-core/tools/releases/tag/2.10). ## 1.0.0 - White Silver Reebok From 6d71c38fc54c80fc9eab7c47b3bddaed87e78e14 Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Fri, 29 Sep 2023 11:25:55 +0200 Subject: [PATCH 4/4] Escape properly bash command --- modules/local/download_pdbmmcif.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/download_pdbmmcif.nf b/modules/local/download_pdbmmcif.nf index 61e2977f..7cb1d3ce 100644 --- a/modules/local/download_pdbmmcif.nf +++ b/modules/local/download_pdbmmcif.nf @@ -41,7 +41,7 @@ process DOWNLOAD_PDBMMCIF { raw echo "Unzipping all mmCIF files..." - find ./raw -type f -name '*.[gG][zZ]' -print0 | while IFS= read -r -d $'\0' file; do + find ./raw -type f -name '*.[gG][zZ]' -print0 | while IFS= read -r -d \$'\\0' file; do gunzip "$file" done