From 412efec98f38b2cf5a2a802bf42de3a00349960c Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Fri, 11 Jun 2021 12:11:47 +0200 Subject: [PATCH 1/2] fix: tables for TSV files content --- docs/usage.md | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index 685d59ed10..a1503ba641 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -216,8 +216,8 @@ The `TSV` file to start with the mapping step (`--step mapping`) with paired-end In this example (`example_fastq.tsv`), there are 3 read groups. -| | | | | | | -|-|-|-|-|-|-| +| | | | | | | | +|-|-|-|-|-|-|-| |SUBJECT_ID|XX|0|SAMPLE_ID|1|/samples/normal1_1.fastq.gz|/samples/normal1_2.fastq.gz| |SUBJECT_ID|XX|0|SAMPLE_ID|2|/samples/normal2_1.fastq.gz|/samples/normal2_2.fastq.gz| |SUBJECT_ID|XX|0|SAMPLE_ID|3|/samples/normal3_1.fastq.gz|/samples/normal3_2.fastq.gz| @@ -230,8 +230,8 @@ Or, for a normal/tumor pair: In this example (`example_pair_fastq.tsv`), there are 3 read groups for the normal sample and 2 for the tumor sample. -| | | | | | | -|-|-|-|-|-|-| +| | | | | | | | +|-|-|-|-|-|-|-| |SUBJECT_ID|XX|0|SAMPLE_ID1|1|/samples/normal1_1.fastq.gz|/samples/normal1_2.fastq.gz| |SUBJECT_ID|XX|0|SAMPLE_ID1|2|/samples/normal2_1.fastq.gz|/samples/normal2_2.fastq.gz| |SUBJECT_ID|XX|0|SAMPLE_ID1|3|/samples/normal3_1.fastq.gz|/samples/normal3_2.fastq.gz| @@ -327,8 +327,8 @@ The `TSV` contains the following columns: Or, for a normal/tumor pair: -| | | | | | | -|-|-|-|-|-|-| +| | | | | | | | +|-|-|-|-|-|-|-| |SUBJECT_ID|XX|0|SAMPLE_ID1|/samples/normal.md.bam|/samples/normal.md.bai|/samples/normal.recal.table| |SUBJECT_ID|XX|1|SAMPLE_ID2|/samples/tumor.md.bam|/samples/tumor.md.bai|/samples/tumor.recal.table| From e54a7783a2339a25394d166c0f39f836cf07d228 Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Fri, 11 Jun 2021 12:16:13 +0200 Subject: [PATCH 2/2] feat: update CHANGELOG --- CHANGELOG.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index fb632b0919..59f9c0b516 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -18,12 +18,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#373](https://github.com/nf-core/sarek/pull/373) - Sync `TEMPLATE` with `tools` 1.14 - [#376](https://github.com/nf-core/sarek/pull/376) - Better logo on Github dark Mode -- [#383](https://github.com/nf-core/sarek/pull/383) - Update CHANGELOG +- [#387](https://github.com/nf-core/sarek/pull/387) - Fix tables for TSV file content ### Fixed - [#375](https://github.com/nf-core/sarek/pull/375), [#381](https://github.com/nf-core/sarek/pull/381), [#382](https://github.com/nf-core/sarek/pull/382), [#385](https://github.com/nf-core/sarek/pull/385) - Fix bugs due to `TEMPLATE` sync from [#373](https://github.com/nf-core/sarek/pull/373) - [#378](https://github.com/nf-core/sarek/pull/378) - Fix `Spark` related issue due to `Docker` settings in `nextflow.config` +- [#378](https://github.com/nf-core/sarek/pull/378) - Fix `Spark` related issue due to `Docker` settings in `nextflow.config` ### Deprecated