From 10ade27c430246f8c2a92e1fc12c963a93c8115a Mon Sep 17 00:00:00 2001 From: Alexandre Gilardet Date: Mon, 8 Mar 2021 16:36:45 +0000 Subject: [PATCH 1/4] added default -doMajorMinor 1 to output angsd beagle format + corrected typo in error message about angsd output format --- main.nf | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/main.nf b/main.nf index 88ebe9e4d..ce4b4040b 100644 --- a/main.nf +++ b/main.nf @@ -456,7 +456,7 @@ if (params.run_genotyping){ } if (params.genotyping_tool == 'angsd' && ! ( params.angsd_glformat == 'text' || params.angsd_glformat == 'binary' || params.angsd_glformat == 'binary_three' || params.angsd_glformat == 'beagle' ) ) { - exit 1, "[nf-core/eager] error: please check your ANGSD genotyping model! Options: 'text', 'binary', 'binary_three', 'beagle'. Found parameter: --angsd_glmodel '${params.angsd_glmodel}'." + exit 1, "[nf-core/eager] error: please check your ANGSD output format! Options: 'text', 'binary', 'binary_three', 'beagle'. Found parameter: --angsd_glformat '${params.angsd_glformat}'." } if ( !params.angsd_createfasta && params.angsd_fastamethod != 'random' ) { @@ -2762,10 +2762,11 @@ process genotyping_angsd { } def angsd_fasta = !params.angsd_createfasta ? '' : params.angsd_fastamethod == 'random' ? '-doFasta 1 -doCounts 1' : '-doFasta 2 -doCounts 1' + def angsd_majorminor = params.angsd_glformat != "beagle" ? '' : '-doMajorMinor 1' """ echo ${bam} > bam.filelist mkdir angsd - angsd -bam bam.filelist -nThreads ${task.cpus} -GL ${angsd_glmodel} -doGlF ${angsd_glformat} ${angsd_fasta} -out ${samplename}.angsd + angsd -bam bam.filelist -nThreads ${task.cpus} -GL ${angsd_glmodel} -doGlF ${angsd_glformat} ${angsd_majorminor} ${angsd_fasta} -out ${samplename}.angsd """ } From 069267af950cd5187f24b85eacb06364cd7c7e4f Mon Sep 17 00:00:00 2001 From: Alexandre Gilardet Date: Tue, 9 Mar 2021 10:05:00 +0000 Subject: [PATCH 2/4] Changed CHANGELOG.md for #690 --- CHANGELOG.md | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 2e4985f0d..12f91792e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,30 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html). +## [dev] - unreleased + +### `Added` + +### `Fixed` + +- [#690](https://github.com/nf-core/eager/pull/690) - Fixed ANGSD output mode for beagle by setting `-doMajorMinor 1` as default in that case +- [#666](https://github.com/nf-core/eager/issues/666) - Fixed input file staging for `print_nuclear_contamination` +- [#631](https://github.com/nf-core/eager/issues/631) - Update minimum Nextflow version to 20.07.1, due to unfortunate bug in Nextflow 20.04.1 causing eager to crash if patch pulled +- Made MultiQC crash behaviour stricter when dealing with large datasets, as reported by @ashildv +- [#652](https://github.com/nf-core/eager/issues/652) Added note to documentation that when using `--skip_collapse` this will use _paired-end_ alignment mode with mappers when using PE data +- [#626](https://github.com/nf-core/eager/issues/626) - Add additional checks to ensure pipeline will give useful error if cells of a TSV column are empty +- Added note to documentation that when using `--skip_collapse` this will use _paired-end_ alignment mode with mappers when using PE data. ` +- [#673](https://github.com/nf-core/eager/pull/673) Fix Kraken database loading when loading from directory instead of compressed file. +- [#688](https://github.com/nf-core/eager/issues/668) - Allow pipeline to complete, even if Qualimap crashes due to an empty or corrupt BAM file for one sample/library +- [#683](https://github.com/nf-core/eager/pull/683) - Sets `--igenomes_ignore` to true by default, as rarely used by users currently and makes resolving configs less complex. +- Added exit code `140` to re-tryable exit code list to account for certain scheduler wall-time limit fails. +- [672](https://github.com/nf-core/eager/issues/672) - Removed java parameter from picard tools which could cause memory issues +- [679](https://github.com/nf-core/eager/issues/679) - Refactor within-process bash conditions to groovy/nextflow, due to incompatibility with some servers environments + +### `Dependencies` + +### `Deprecated` + ## [2.3.1] - 2021-01-14 ### `Added` From 2185f798188c4d12f1dc7325d602b08914bcca4b Mon Sep 17 00:00:00 2001 From: Alexandre Gilardet Date: Wed, 10 Mar 2021 10:00:05 +0000 Subject: [PATCH 3/4] corrected CHANGELOG.md dev section --- CHANGELOG.md | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 79831bd45..a52722f5c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,10 +9,25 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. ### `Fixed` +- [#666](https://github.com/nf-core/eager/issues/666) - Fixed input file staging for `print_nuclear_contamination` +- [#631](https://github.com/nf-core/eager/issues/631) - Update minimum Nextflow version to 20.07.1, due to unfortunate bug in Nextflow 20.04.1 causing eager to crash if patch pulled +- Made MultiQC crash behaviour stricter when dealing with large datasets, as reported by @ashildv +- [#652](https://github.com/nf-core/eager/issues/652) Added note to documentation that when using `--skip_collapse` this will use _paired-end_ alignment mode with mappers when using PE data +- [#626](https://github.com/nf-core/eager/issues/626) - Add additional checks to ensure pipeline will give useful error if cells of a TSV column are empty +- Added note to documentation that when using `--skip_collapse` this will use _paired-end_ alignment mode with mappers when using PE data. ` +- [#673](https://github.com/nf-core/eager/pull/673) Fix Kraken database loading when loading from directory instead of compressed file. +- [#688](https://github.com/nf-core/eager/issues/668) - Allow pipeline to complete, even if Qualimap crashes due to an empty or corrupt BAM file for one sample/library +- [#683](https://github.com/nf-core/eager/pull/683) - Sets `--igenomes_ignore` to true by default, as rarely used by users currently and makes resolving configs less complex. +- Added exit code `140` to re-tryable exit code list to account for certain scheduler wall-time limit fails. +- [672](https://github.com/nf-core/eager/issues/672) - Removed java parameter from picard tools which could cause memory issues +- [679](https://github.com/nf-core/eager/issues/679) - Refactor within-process bash conditions to groovy/nextflow, due to incompatibility with some servers environments - [#690](https://github.com/nf-core/eager/pull/690) - Fixed ANGSD output mode for beagle by setting `-doMajorMinor 1` as default in that case + ### `Dependencies` +- Bumped MultiQC to 1.10 for improved functionality + ### `Deprecated` ## [2.3.1] - 2021-01-14 From cb848822930f6e19a039fd65e54e95b5b7d950be Mon Sep 17 00:00:00 2001 From: Alexandre Gilardet Date: Wed, 10 Mar 2021 10:02:01 +0000 Subject: [PATCH 4/4] corrected CHANGELOG.md dev section --- CHANGELOG.md | 1 - 1 file changed, 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index a52722f5c..b4df74905 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -23,7 +23,6 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. - [679](https://github.com/nf-core/eager/issues/679) - Refactor within-process bash conditions to groovy/nextflow, due to incompatibility with some servers environments - [#690](https://github.com/nf-core/eager/pull/690) - Fixed ANGSD output mode for beagle by setting `-doMajorMinor 1` as default in that case - ### `Dependencies` - Bumped MultiQC to 1.10 for improved functionality