Fix/readme 391

.github/workflows/ci.yml

@@ -25,7 +25,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        shard: [1, 2, 3, 4]
+        shard: [1, 2, 3, 4, 5]
         NXF_VER: ["latest-stable"] # TODO Test minimum version on release
         profile: ["docker"]
     steps:
@@ -57,9 +57,8 @@ jobs:
           nf-test test \
               --ci \
               --shard ${{ matrix.shard }}/${{ strategy.job-total }} \
-              --changed-until feat/workflow-updates \
-              --profile "+${{ matrix.profile }}" \
-              --filter pipeline
+              --changed-since HEAD^ \
+              --profile "+${{ matrix.profile }}"
 
       - name: Publish Test Report
         uses: mikepenz/action-junit-report@v3

README.md

@@ -55,11 +55,11 @@ First, prepare a samplesheet with your input data that looks as follows:
 `samplesheet.csv`:
 
 ```csv
-sample,fastq_1,fastq_2
-SRR389222_sub1,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub1.fastq.gz
-SRR389222_sub2,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub2.fastq.gz
-SRR389222_sub2,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub3.fastq.gz
-Ecoli_10K_methylated,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R1.fastq.gz,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R2.fastq.gz
+sample,fastq_1,fastq_2,genome
+SRR389222_sub1,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub1.fastq.gz,,
+SRR389222_sub2,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub2.fastq.gz,,
+SRR389222_sub3,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub3.fastq.gz,,
+Ecoli_10K_methylated,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R1.fastq.gz,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R2.fastq.gz,
 ```
 
 Each row represents a fastq file (single-end) or a pair of fastq files (paired end).

assets/samplesheet.csv

@@ -2,4 +2,4 @@ sample,fastq_1,fastq_2,genome
 SRR389222_sub1,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub1.fastq.gz,,
 SRR389222_sub2,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub2.fastq.gz,,
 SRR389222_sub3,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub3.fastq.gz,,
-Ecoli,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R1.fastq.gz,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R2.fastq.gz,
+Ecoli_10K_methylated,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R1.fastq.gz,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R2.fastq.gz,

docs/usage.md

@@ -8,10 +8,10 @@
 
 - [Table of contents](#table-of-contents)
 - [Introduction](#introduction)
-  - [Bismark and bwa-meth workflow](#bismark-and-bwa-meth-workflow)
+- [Bismark and bwa-meth workflow](#bismark-and-bwa-meth-workflow)
 - [Running the pipeline](#running-the-pipeline)
-  - [Updating the pipeline](#updating-the-pipeline)
-  - [Reproducibility](#reproducibility)
+- [Updating the pipeline](#updating-the-pipeline)
+- [Reproducibility](#reproducibility)
 
 ## Introduction
 
@@ -23,21 +23,26 @@ The second workflow uses [BWA-Meth](https://github.com/brentp/bwa-meth) and [Met
 
 ## Samplesheet input
 
-You will need to create a samplesheet with information about the samples you would like to analyse before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row as shown in the examples below.
+You will need to create a samplesheet with information about the samples you would like to analyse before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 4 columns, and a header row as shown in the examples below.
 
 ```bash
 --input '[path to samplesheet file]'
 ```
 
+```csv title="header.csv"
+sample,fastq_1,fastq_2,genome
+```
+
 ### Multiple runs of the same sample
 
 The `sample` identifiers have to be the same when you have re-sequenced the same sample more than once e.g. to increase sequencing depth. The pipeline will concatenate the raw reads before performing any downstream analysis. Below is an example for the same sample sequenced across 3 lanes:
 
 ```csv title="samplesheet.csv"
-sample,fastq_1,fastq_2
-CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz
-CONTROL_REP1,AEG588A1_S1_L003_R1_001.fastq.gz,AEG588A1_S1_L003_R2_001.fastq.gz
-CONTROL_REP1,AEG588A1_S1_L004_R1_001.fastq.gz,AEG588A1_S1_L004_R2_001.fastq.gz
+sample,fastq_1,fastq_2,genome
+SRR389222_sub1,SRR389222_sub1.fastq.gz,,
+SRR389222_sub2,SRR389222_sub2.fastq.gz,,
+SRR389222_sub3,SRR389222_sub3.fastq.gz,,
+Ecoli_10K_methylated,Ecoli_10K_methylated_R1.fastq.gz,Ecoli_10K_methylated_R2.fastq.gz,
 ```
 
 ### Full samplesheet
@@ -47,21 +52,22 @@ The pipeline will auto-detect whether a sample is single- or paired-end using th
 A final samplesheet file consisting of both single- and paired-end data may look something like the one below. This is for 6 samples, where `TREATMENT_REP3` has been sequenced twice.
 
 ```csv title="samplesheet.csv"
-sample,fastq_1,fastq_2
-CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz
-CONTROL_REP2,AEG588A2_S2_L002_R1_001.fastq.gz,AEG588A2_S2_L002_R2_001.fastq.gz
-CONTROL_REP3,AEG588A3_S3_L002_R1_001.fastq.gz,AEG588A3_S3_L002_R2_001.fastq.gz
-TREATMENT_REP1,AEG588A4_S4_L003_R1_001.fastq.gz,
-TREATMENT_REP2,AEG588A5_S5_L003_R1_001.fastq.gz,
-TREATMENT_REP3,AEG588A6_S6_L003_R1_001.fastq.gz,
-TREATMENT_REP3,AEG588A6_S6_L004_R1_001.fastq.gz,
+sample,fastq_1,fastq_2,genome
+CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,
+CONTROL_REP2,AEG588A2_S2_L002_R1_001.fastq.gz,AEG588A2_S2_L002_R2_001.fastq.gz,
+CONTROL_REP3,AEG588A3_S3_L002_R1_001.fastq.gz,AEG588A3_S3_L002_R2_001.fastq.gz,
+TREATMENT_REP1,AEG588A4_S4_L003_R1_001.fastq.gz,,
+TREATMENT_REP2,AEG588A5_S5_L003_R1_001.fastq.gz,,
+TREATMENT_REP3,AEG588A6_S6_L003_R1_001.fastq.gz,,
+TREATMENT_REP3,AEG588A6_S6_L004_R1_001.fastq.gz,,
 ```
 
 | Column    | Description                                                                                                                                                                            |
 | --------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
 | `sample`  | Custom sample name. This entry will be identical for multiple sequencing libraries/runs from the same sample. Spaces in sample names are automatically converted to underscores (`_`). |
 | `fastq_1` | Full path to FastQ file for Illumina short reads 1. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz".                                                             |
 | `fastq_2` | Full path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz".                                                             |
+| `genome`  | Reference genome to be used (OPTIONAL)                                                                                                                                                 |
 
 An [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline.
 

modules.json

@@ -102,27 +102,27 @@
                     },
                     "samtools/faidx": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
                         "installed_by": ["modules"]
                     },
                     "samtools/flagstat": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
                         "installed_by": ["modules"]
                     },
                     "samtools/index": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
                         "installed_by": ["modules"]
                     },
                     "samtools/sort": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
                         "installed_by": ["modules"]
                     },
                     "samtools/stats": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
                         "installed_by": ["modules"]
                     },
                     "trimgalore": {