Skip to content

fix: tables for TSV files content #387

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
maxulysse merged 2 commits into from
Jun 11, 2021
Merged

fix: tables for TSV files content #387

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
412efec
fix: tables for TSV files content
maxulysse Jun 11, 2021
e54a778
feat: update CHANGELOG
maxulysse Jun 11, 2021
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
3 changes: 2 additions & 1 deletion CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
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

Expand Down
12 changes: 6 additions & 6 deletions docs/usage.md
View file
Open in desktop
Original file line number Diff line number Diff line change
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|

Expand Down
⚡