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Replace < and > by HTML codes #280

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Sep 4, 2020
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Replace < and > by HTML codes #280

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121b657
replace < and > by HTML codes
maxulysse Sep 4, 2020
f15c48b
update CHANGELOG
maxulysse Sep 4, 2020
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -28,6 +28,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
- [#271](https://github.com/nf-core/sarek/pull/271) - Fix `ConcatVCF_Mutect2` `SIGPIPE` issue [#268](https://github.com/nf-core/sarek/issues/268)
- [#272](https://github.com/nf-core/sarek/pull/272) - Fix annotation `--tools merge` issue
- [#279](https://github.com/nf-core/sarek/pull/279) - Fix issue with `--step prepare_recalibration` [#267](https://github.com/nf-core/sarek/issues/267)
- [#280](https://github.com/nf-core/sarek/pull/280) - Use HTML codes instead of `<` and `>` in docs

### Removed

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40 changes: 20 additions & 20 deletions docs/usage.md
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Expand Up @@ -13,16 +13,16 @@
- [Pipeline specific arguments](#pipeline-specific-arguments)
- [--step](#--step)
- [--input](#--input)
- [--input \<FASTQ\> --step mapping](#--input-fastq---step-mapping)
- [--input \<uBAM\> --step mapping](#--input-ubam---step-mapping)
- [--input \<sample/\> --step mapping](#--input-sample---step-mapping)
- [--input \<TSV\> --step prepare_recalibration](#--input-tsv---step-prepare_recalibration)
- [--input \<TSV\> --step prepare_recalibration --skip_markduplicates](#--input-tsv---step-prepare_recalibration---skip_markduplicates)
- [--input \<TSV\> --step recalibrate](#--input-tsv---step-recalibrate)
- [--input \<TSV\> --step recalibrate --skip_markduplicates](#--input-tsv---step-recalibrate---skip_markduplicates)
- [--input \<TSV\> --step variant_calling](#--input-tsv---step-variant_calling)
- [--input \<TSV\> --step Control-FREEC](#--input-tsv---step-control-freec)
- [--input \<VCF\> --step annotate](#--input-vcf---step-annotate)
- [--input &lt;FASTQ&gt; --step mapping](#--input-fastq---step-mapping)
- [--input &lt;uBAM&gt; --step mapping](#--input-ubam---step-mapping)
- [--input &lt;sample/&gt; --step mapping](#--input-sample---step-mapping)
- [--input &lt;TSV&gt; --step prepare_recalibration](#--input-tsv---step-prepare_recalibration)
- [--input &lt;TSV&gt; --step prepare_recalibration --skip_markduplicates](#--input-tsv---step-prepare_recalibration---skip_markduplicates)
- [--input &lt;TSV&gt; --step recalibrate](#--input-tsv---step-recalibrate)
- [--input &lt;TSV&gt; --step recalibrate --skip_markduplicates](#--input-tsv---step-recalibrate---skip_markduplicates)
- [--input &lt;TSV&gt; --step variant_calling](#--input-tsv---step-variant_calling)
- [--input &lt;TSV&gt; --step Control-FREEC](#--input-tsv---step-control-freec)
- [--input &lt;VCF&gt; --step annotate](#--input-vcf---step-annotate)
- [--help](#--help)
- [--no_intervals](#--no_intervals)
- [--nucleotides_per_second](#--nucleotides_per_second)
Expand Down Expand Up @@ -355,7 +355,7 @@ Multiple `TSV` files can be specified if the path is enclosed in quotes.

Output from Variant Calling and/or Annotation will be in a specific directory for each sample (or normal/tumor pair if applicable).

#### --input \<FASTQ\> --step mapping
#### --input &lt;FASTQ&gt; --step mapping

The `TSV` file to start with the step mapping with paired-end `FASTQs` should contain the columns:

Expand Down Expand Up @@ -389,7 +389,7 @@ In this example (`example_pair_fastq.tsv`), there are 3 read groups for the norm
--input example_pair_fastq.tsv
```

#### --input \<uBAM\> --step mapping
#### --input &lt;uBAM&gt; --step mapping

The `TSV` file for starting the mapping from `unmapped BAM` files should contain the columns:

Expand Down Expand Up @@ -423,7 +423,7 @@ In this example (`example_pair_ubam.tsv`), there are 3 read groups for the norma
--input example_pair_ubam.tsv
```

#### --input \<sample/\> --step mapping
#### --input &lt;sample/&gt; --step mapping

Use this to specify the location to a directory with `FASTQ` files for the `mapping` step of a single germline sample only.
For example:
Expand Down Expand Up @@ -481,7 +481,7 @@ That is, you should make sure that that directory has a meaningful name! For exa
- The read group id is set to *flowcell.samplename.lane*.
The flowcell id and lane number are auto-detected from the name of the first read in the `FASTQ` file.

#### --input \<TSV\> --step prepare_recalibration
#### --input &lt;TSV&gt; --step prepare_recalibration

To start from the preparation of the recalibration step (`--step prepare_recalibration`), a `TSV` file needs to be given as input containing the paths to the `non-recalibrated BAM` files.
The `Sarek`-generated `TSV` file is stored under `results/Preprocessing/TSV/duplicates_marked_no_table.tsv` and will automatically be used as an input when specifying the parameter `--step prepare_recalibration`.
Expand All @@ -501,7 +501,7 @@ Or, for a normal/tumor pair:
|SUBJECT_ID|XX|0|SAMPLE_ID1|/samples/normal.md.bam|/samples/normal.md.bai|
|SUBJECT_ID|XX|1|SAMPLE_ID2|/samples/tumor.md.bam|/samples/tumor.md.bai|

#### --input \<TSV\> --step prepare_recalibration --skip_markduplicates
#### --input &lt;TSV&gt; --step prepare_recalibration --skip_markduplicates

The `Sarek`-generated `TSV` file is stored under `results/Preprocessing/TSV/mapped.tsv` and will automatically be used as an input when specifying the parameter `--step prepare_recalibration --skip_markduplicates`.
The `TSV` file contains the same columns, but the content is slightly different:
Expand All @@ -517,7 +517,7 @@ Or, for a normal/tumor pair:
|SUBJECT_ID|XX|0|SAMPLE_ID1|/samples/normal.bam|/samples/normal.bai|
|SUBJECT_ID|XX|1|SAMPLE_ID2|/samples/tumor.bam|/samples/tumor.bai|

#### --input \<TSV\> --step recalibrate
#### --input &lt;TSV&gt; --step recalibrate

To start from the recalibrate step (`--step recalibrate`), a `TSV` file needs to be given as input containing the paths to the `non-recalibrated BAM` file and the associated recalibration table.
The `Sarek`-generated `TSV` file is stored under `results/Preprocessing/TSV/duplicates_marked.tsv` and will automatically be used as an input when specifying the parameter `--step recalibrate`.
Expand All @@ -537,7 +537,7 @@ 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|

#### --input \<TSV\> --step recalibrate --skip_markduplicates
#### --input &lt;TSV&gt; --step recalibrate --skip_markduplicates

The `Sarek`-generated `TSV` file is stored under `results/Preprocessing/TSV/mapped_no_duplicates_marked.tsv` and will automatically be used as an input when specifying the parameter `--step recalibrate --skip_markduplicates`.
The `TSV` file contains the same columns, but the content is slightly different:
Expand All @@ -553,7 +553,7 @@ Or, for a normal/tumor pair:
|SUBJECT_ID|XX|0|SAMPLE_ID1|/samples/normal.bam|/samples/normal.bai|/samples/normal.recal.table|
|SUBJECT_ID|XX|1|SAMPLE_ID2|/samples/tumor.bam|/samples/tumor.bai|/samples/tumor.recal.table|

#### --input \<TSV\> --step variant_calling
#### --input &lt;TSV&gt; --step variant_calling

To start from the variant calling step (`--step variant_calling`), a `TSV` file needs to be given as input containing the paths to the `recalibrated BAM` file and the associated index.
The `Sarek`-generated `TSV` file is stored under `results/Preprocessing/TSV/recalibrated.tsv` and will automatically be used as an input when specifying the parameter `--step variant_calling`.
Expand All @@ -575,7 +575,7 @@ Or, for a normal/tumor pair:
|SUBJECT_ID|XX|0|SAMPLE_ID1|/samples/normal.recal.bam|/samples/normal.recal.bai|
|SUBJECT_ID|XX|1|SAMPLE_ID2|/samples/tumor.recal.bam|/samples/tumor.recal.bai|

#### --input \<TSV\> --step Control-FREEC
#### --input &lt;TSV&gt; --step Control-FREEC

To start from the Control-FREEC step (`--step Control-FREEC`), a `TSV` file needs to be given as input containing the paths to the mpileup files.
The `Sarek`-generated `TSV` file is stored under `results/VariantCalling/TSV/control-freec_mpileup.tsv` and will automatically be used as an input when specifying the parameter `--step Control-FREEC`.
Expand All @@ -591,7 +591,7 @@ Here is an example for one normal/tumor pair from one subjects:
|SUBJECT_ID|XX|0|SAMPLE_ID1|/samples/normal.pileup|
|SUBJECT_ID|XX|1|SAMPLE_ID2|/samples/tumor.pileup|

#### --input \<VCF\> --step annotate
#### --input &lt;VCF&gt; --step annotate

Input files for Sarek can be specified using the path to a `VCF` file given to the `--input` command only with the annotation step (`--step annotate`).
As `Sarek` will use `bgzip` and `tabix` to compress and index `VCF` files annotated, it expects `VCF` files to be sorted.
Expand Down