From 7405c8ece148227eae671375a026ccec34ed00a3 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Mon, 25 Feb 2019 17:21:54 +0100 Subject: [PATCH 1/5] Fix for post-dup steps --- CHANGELOG.md | 1 + main.nf | 4 ++-- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 047f5b207..28b97779b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -15,6 +15,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. ### `Fixed` * [#128](https://github.com/nf-core/eager/issues/128) - Fixed reference genome handling errors +* [#140](https://github.com/nf-core/eager/issues/140) - Fixed post-deduplication step errors ### `Dependencies` * Picard Tools 2.18.21 -> 2.18.23 diff --git a/main.nf b/main.nf index 826b0bff5..d0e0c4f38 100644 --- a/main.nf +++ b/main.nf @@ -907,7 +907,7 @@ process damageprofiler { input: file bam from ch_mapped_reads_damageprofiler.mix(ch_mapped_reads_damageprofiler_cm,ch_bwamem_mapped_reads_damageprofiler) - file fasta from ch_fasta_for_damageprofiler + file fasta from ch_fasta_for_damageprofiler.first() file bai from ch_bam_index_for_damageprofiler @@ -934,7 +934,7 @@ process qualimap { input: file bam from ch_bam_filtered_qualimap - file fasta from ch_fasta_for_qualimap + file fasta from ch_fasta_for_qualimap.first() output: file "*" into ch_qualimap_results From 7e4035d74f119be16b3bf0b4838dc41c6fda7acd Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Mon, 25 Feb 2019 17:24:24 +0100 Subject: [PATCH 2/5] Nicer changelog [skip ci] --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 28b97779b..a5b579f5e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -15,7 +15,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. ### `Fixed` * [#128](https://github.com/nf-core/eager/issues/128) - Fixed reference genome handling errors -* [#140](https://github.com/nf-core/eager/issues/140) - Fixed post-deduplication step errors +* [#151](https://github.com/nf-core/eager/pull/151) - Fixed [post-deduplication step errors](https://github.com/nf-core/eager/issues/128) ### `Dependencies` * Picard Tools 2.18.21 -> 2.18.23 From 76e0cbd859f935196e03dcc5003f5e33257d9781 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Mon, 25 Feb 2019 17:25:44 +0100 Subject: [PATCH 3/5] Its unpublished stuff [skip ci] --- CHANGELOG.md | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index a5b579f5e..9389bdc0b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,6 +6,9 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. ## [Unpublished / Dev Branch] +### `Fixed` +* [#151](https://github.com/nf-core/eager/pull/151) - Fixed [post-deduplication step errors](https://github.com/nf-core/eager/issues/128 + ## [2.0.5] - 2019-01-28 ### `Added` @@ -15,7 +18,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. ### `Fixed` * [#128](https://github.com/nf-core/eager/issues/128) - Fixed reference genome handling errors -* [#151](https://github.com/nf-core/eager/pull/151) - Fixed [post-deduplication step errors](https://github.com/nf-core/eager/issues/128) +) ### `Dependencies` * Picard Tools 2.18.21 -> 2.18.23 From fabd1a3dbdcb715211dcf9d70494b2d57295cd7a Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Wed, 27 Feb 2019 00:08:51 +0100 Subject: [PATCH 4/5] Should fix the remaining issues --- main.nf | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/main.nf b/main.nf index d0e0c4f38..5c053ef28 100644 --- a/main.nf +++ b/main.nf @@ -1139,12 +1139,12 @@ process multiqc { file multiqc_config from ch_multiqc_config.collect().ifEmpty([]) file ('fastqc_raw/*') from ch_fastqc_results.collect().ifEmpty([]) file('fastqc/*') from ch_fastqc_after_clipping.collect().ifEmpty([]) - file ('software_versions/*') from software_versions_yaml.collect().ifEmpty([]) + file ('software_versions/software_versions_mqc*') from software_versions_yaml.collect().ifEmpty([]) file ('adapter_removal/*') from ch_adapterremoval_logs.collect().ifEmpty([]) file ('idxstats/*') from ch_idxstats_for_multiqc.collect().ifEmpty([]) file ('preseq/*') from ch_preseq_results.collect().ifEmpty([]) - file ('damageprofiler/*') from ch_damageprofiler_results.collect().ifEmpty([]) - file ('qualimap/*') from ch_qualimap_results.collect().ifEmpty([]) + file ('damageprofiler/dmgprof*') from ch_damageprofiler_results.collect().ifEmpty([]) + file ('qualimap*') from ch_qualimap_results.collect().ifEmpty([]) file ('markdup/*') from ch_markdup_results_for_multiqc.collect().ifEmpty([]) file ('dedup*/*') from ch_dedup_results_for_multiqc.collect().ifEmpty([]) file ('fastp/*') from ch_fastp_for_multiqc.collect().ifEmpty([]) From c69261d268b2633dee44e4f518d0544e6f45b048 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Wed, 27 Feb 2019 00:17:58 +0100 Subject: [PATCH 5/5] Address issues with qualimap / multiqc / multiple samples and reporting --- main.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/main.nf b/main.nf index f30b22ea2..b594697c7 100644 --- a/main.nf +++ b/main.nf @@ -1144,8 +1144,8 @@ process multiqc { file ('adapter_removal/*') from ch_adapterremoval_logs.collect().ifEmpty([]) file ('idxstats/*') from ch_idxstats_for_multiqc.collect().ifEmpty([]) file ('preseq/*') from ch_preseq_results.collect().ifEmpty([]) - file ('damageprofiler/dmgprof*') from ch_damageprofiler_results.collect().ifEmpty([]) - file ('qualimap*') from ch_qualimap_results.collect().ifEmpty([]) + file ('damageprofiler/dmgprof*/*') from ch_damageprofiler_results.collect().ifEmpty([]) + file ('qualimap/qualimap*/*') from ch_qualimap_results.collect().ifEmpty([]) file ('markdup/*') from ch_markdup_results_for_multiqc.collect().ifEmpty([]) file ('dedup*/*') from ch_dedup_results_for_multiqc.collect().ifEmpty([]) file ('fastp/*') from ch_fastp_for_multiqc.collect().ifEmpty([])