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fix: tables for TSV files content #387

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Jun 11, 2021
Merged

fix: tables for TSV files content #387

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412efec
fix: tables for TSV files content
maxulysse Jun 11, 2021
e54a778
feat: update CHANGELOG
maxulysse Jun 11, 2021
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3 changes: 2 additions & 1 deletion CHANGELOG.md
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Expand Up @@ -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

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12 changes: 6 additions & 6 deletions docs/usage.md
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Expand Up @@ -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|
Expand All @@ -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|
Expand Down Expand Up @@ -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|

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