Merge pull request #340 from JoseEspinosa/docs_fixes

Docs fixes

Author: JoseEspinosa

CHANGELOG.md

@@ -13,6 +13,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [[#311](https://github.com/nf-core/chipseq/issues/311)] Add back `--skip_spp` parameter which was unintentionally removed from the code.
 - Install available nf-core subworkflows and refactor code accordingly
 - [[#318](https://github.com/nf-core/chipseq/issues/318)] Update `bowtie2/align` module to fix issue when downloading its singularity image.
+- [[#320](https://github.com/nf-core/chipseq/issues/320)] Fix samplesheet control column in documentation examples.
+- [[#328](https://github.com/nf-core/chipseq/issues/328)] Modify documentation to clarify that is necessary to provide the `--read_length` when `--genome` is set and `--macs_gsize` has not provided.
 
 ## [[2.0.0](https://github.com/nf-core/chipseq/releases/tag/2.0.0)] - 2022-10-03
 

README.md

@@ -32,7 +32,7 @@ You can find numerous talks on the [nf-core events page](https://nf-co.re/events
 2. Adapter trimming ([`Trim Galore!`](https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/))
 3. Choice of multiple aligners
    1.([`BWA`](https://sourceforge.net/projects/bio-bwa/files/))
-   2.([`Chromap`](https://github.com/haowenz/chromap)). **For paired-end reads only working until mapping steps, see [here](https://github.com/nf-core/chipseq/issues/291)**
+   2.([`Chromap`](https://github.com/haowenz/chromap))
    3.([`Bowtie2`](http://bowtie-bio.sourceforge.net/bowtie2/index.shtml))
    4.([`STAR`](https://github.com/alexdobin/STAR))
 4. Mark duplicates ([`picard`](https://broadinstitute.github.io/picard/))

docs/usage.md

@@ -18,11 +18,11 @@ The `sample` identifiers have to be the same when you have re-sequenced the same
 
 ```console
 sample,fastq_1,fastq_2,antibody,control
-WT_BCATENIN_IP_REP1,BLA203A1_S27_L006_R1_001.fastq.gz,,BCATENIN,WT_INPUT
-WT_BCATENIN_IP_REP2,BLA203A25_S16_L001_R1_001.fastq.gz,,BCATENIN,WT_INPUT
-WT_BCATENIN_IP_REP2,BLA203A25_S16_L002_R1_001.fastq.gz,,BCATENIN,WT_INPUT
-WT_BCATENIN_IP_REP2,BLA203A25_S16_L003_R1_001.fastq.gz,,BCATENIN,WT_INPUT
-WT_BCATENIN_IP_REP3,BLA203A49_S40_L001_R1_001.fastq.gz,,BCATENIN,WT_INPUT
+WT_BCATENIN_IP_REP1,BLA203A1_S27_L006_R1_001.fastq.gz,,BCATENIN,WT_INPUT_REP1
+WT_BCATENIN_IP_REP2,BLA203A25_S16_L001_R1_001.fastq.gz,,BCATENIN,WT_INPUT_REP2
+WT_BCATENIN_IP_REP2,BLA203A25_S16_L002_R1_001.fastq.gz,,BCATENIN,WT_INPUT_REP2
+WT_BCATENIN_IP_REP2,BLA203A25_S16_L003_R1_001.fastq.gz,,BCATENIN,WT_INPUT_REP2
+WT_BCATENIN_IP_REP3,BLA203A49_S40_L001_R1_001.fastq.gz,,BCATENIN,WT_INPUT_REP3
 WT_INPUT_REP1,BLA203A6_S32_L006_R1_001.fastq.gz,,,
 WT_INPUT_REP2,BLA203A30_S21_L001_R1_001.fastq.gz,,,
 WT_INPUT_REP2,BLA203A30_S21_L002_R1_001.fastq.gz,,,
@@ -41,20 +41,20 @@ A final design file may look something like the one below. This is for two antib
 
 ```console
 sample,fastq_1,fastq_2,antibody,control
-WT_BCATENIN_IP_REP1,BLA203A1_S27_L006_R1_001.fastq.gz,,BCATENIN,WT_INPUT
-WT_BCATENIN_IP_REP2,BLA203A25_S16_L001_R1_001.fastq.gz,,BCATENIN,WT_INPUT
-WT_BCATENIN_IP_REP2,BLA203A25_S16_L002_R1_001.fastq.gz,,BCATENIN,WT_INPUT
-WT_BCATENIN_IP_REP3,BLA203A49_S40_L001_R1_001.fastq.gz,,BCATENIN,WT_INPUT
-NAIVE_BCATENIN_IP_REP1,BLA203A7_S60_L001_R1_001.fastq.gz,,BCATENIN,NAIVE_INPUT
-NAIVE_BCATENIN_IP_REP2,BLA203A43_S34_L001_R1_001.fastq.gz,,BCATENIN,NAIVE_INPUT
-NAIVE_BCATENIN_IP_REP2,BLA203A43_S34_L002_R1_001.fastq.gz,,BCATENIN,NAIVE_INPUT
-NAIVE_BCATENIN_IP_REP3,BLA203A64_S55_L001_R1_001.fastq.gz,,BCATENIN,NAIVE_INPUT
-WT_TCF4_IP_REP1,BLA203A3_S29_L006_R1_001.fastq.gz,,TCF4,WT_INPUT
-WT_TCF4_IP_REP2,BLA203A27_S18_L001_R1_001.fastq.gz,,TCF4,WT_INPUT
-WT_TCF4_IP_REP3,BLA203A51_S42_L001_R1_001.fastq.gz,,TCF4,WT_INPUT
-NAIVE_TCF4_IP_REP1,BLA203A9_S62_L001_R1_001.fastq.gz,,TCF4,NAIVE_INPUT
-NAIVE_TCF4_IP_REP2,BLA203A45_S36_L001_R1_001.fastq.gz,,TCF4,NAIVE_INPUT
-NAIVE_TCF4_IP_REP3,BLA203A66_S57_L001_R1_001.fastq.gz,,TCF4,NAIVE_INPUT
+WT_BCATENIN_IP_REP1,BLA203A1_S27_L006_R1_001.fastq.gz,,BCATENIN,WT_INPUT_REP1
+WT_BCATENIN_IP_REP2,BLA203A25_S16_L001_R1_001.fastq.gz,,BCATENIN,WT_INPUT_REP2
+WT_BCATENIN_IP_REP2,BLA203A25_S16_L002_R1_001.fastq.gz,,BCATENIN,WT_INPUT_REP2
+WT_BCATENIN_IP_REP3,BLA203A49_S40_L001_R1_001.fastq.gz,,BCATENIN,WT_INPUT_REP3
+NAIVE_BCATENIN_IP_REP1,BLA203A7_S60_L001_R1_001.fastq.gz,,BCATENIN,NAIVE_INPUT_REP1
+NAIVE_BCATENIN_IP_REP2,BLA203A43_S34_L001_R1_001.fastq.gz,,BCATENIN,NAIVE_INPUT_REP2
+NAIVE_BCATENIN_IP_REP2,BLA203A43_S34_L002_R1_001.fastq.gz,,BCATENIN,NAIVE_INPUT_REP2
+NAIVE_BCATENIN_IP_REP3,BLA203A64_S55_L001_R1_001.fastq.gz,,BCATENIN,NAIVE_INPUT_REP3
+WT_TCF4_IP_REP1,BLA203A3_S29_L006_R1_001.fastq.gz,,TCF4,WT_INPUT_REP1
+WT_TCF4_IP_REP2,BLA203A27_S18_L001_R1_001.fastq.gz,,TCF4,WT_INPUT_REP2
+WT_TCF4_IP_REP3,BLA203A51_S42_L001_R1_001.fastq.gz,,TCF4,WT_INPUT_REP3
+NAIVE_TCF4_IP_REP1,BLA203A9_S62_L001_R1_001.fastq.gz,,TCF4,NAIVE_INPUT_REP1
+NAIVE_TCF4_IP_REP2,BLA203A45_S36_L001_R1_001.fastq.gz,,TCF4,NAIVE_INPUT_REP2
+NAIVE_TCF4_IP_REP3,BLA203A66_S57_L001_R1_001.fastq.gz,,TCF4,NAIVE_INPUT_REP3
 WT_INPUT_REP1,BLA203A6_S32_L006_R1_001.fastq.gz,,,
 WT_INPUT_REP2,BLA203A30_S21_L001_R1_001.fastq.gz,,,
 WT_INPUT_REP3,BLA203A31_S21_L003_R1_001.fastq.gz,,,

nextflow_schema.json

@@ -37,6 +37,7 @@
                     "type": "integer",
                     "description": "Read length used to calculate MACS2 genome size for peak calling if `--macs_gsize` isn't provided.",
                     "fa_icon": "fas fa-chart-area",
+                    "help_text": "Read length together with the genome fasta are used to calculate MACS2 genome size using the `khmer` program as explained [here](https://deeptools.readthedocs.io/en/develop/content/feature/effectiveGenomeSize.html#effective-genome-size). For all the genomes present in the `igenomes.config` the genome size has been already precomputed and the read length is then used to retrieve the corresponding value",
                     "enum": [50, 75, 100, 150, 200]
                 },
                 "outdir": {
@@ -132,7 +133,7 @@
                 "macs_gsize": {
                     "type": "number",
                     "description": "Effective genome size parameter required by MACS2.",
-                    "help_text": "[Effective genome size](https://github.com/taoliu/MACS#-g--gsize) parameter required by MACS2. If using an iGenomes reference these have been provided when `--genome` is set as *GRCh37*, *GRCh38*, *GRCm38*, *WBcel235*, *BDGP6*, *R64-1-1*, *EF2*, *hg38*, *hg19* and *mm10*. For other genomes, if this parameter is not specified then the MACS2 peak-calling and differential analysis will be skipped.",
+                    "help_text": "[Effective genome size](https://github.com/taoliu/MACS#-g--gsize) parameter required by MACS2. If using an iGenomes reference these have been provided for any of the genomes available in the igenomes.config, and for the following read lengths (50,75,100,150,200) that should be set using the `--read_length` parameter. For other genomes, if this parameter is not specified it will be inferred using the provided `--read_length` or otherwise the pipeline execution will stop with an error.",
                     "fa_icon": "fas fa-arrows-alt-h"
                 },
                 "blacklist": {