Dev -> Master for 2.1.0 release #413

JoseEspinosa · 2024-09-17T14:36:20Z

No description provided.

Some fixes

…omap is used with PE reads

Docs fixes

Get rid of oras from module images

JoseEspinosa · 2024-09-30T12:08:26Z

CHANGELOG.md

@@ -3,6 +3,62 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

+## v2.1.0 - [date]


Update date when releasing!

I also missed in mine.....how do you do this? just direct commit to dev ?

sateeshperi · 2024-09-30T14:10:51Z

modules/local/annotate_boolean_peaks.nf

@@ -2,10 +2,10 @@ process ANNOTATE_BOOLEAN_PEAKS {
    tag "$meta.id"
    label 'process_low'

-    conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
+    conda "conda-forge::sed=4.7"


should the conda be reading from a environment.yml file ?

Yes, you are right but this now will need to refactor all the local modules and I want to release as it is long time we have not done it. If you don't mind I opened an issue to do it for next release, see here

sateeshperi · 2024-09-30T14:16:21Z

modules/local/star_genomegenerate.nf

why have local versions of these nf-core modules ?

The reason is this: the indexes produced by the nf-core modules will be incompatible with iGenomes.

sateeshperi · 2024-09-30T14:26:29Z

nextflow.config

-    version         = '2.0.0'
+    nextflowVersion = '!>=23.04.0'
+    version         = '2.1.0'
+    doi             = ''


forgot DOI or n/a ?

conf/modules.config

README.md

bjlang · 2024-09-27T12:32:18Z

nextflow_schema.json

@@ -100,45 +105,53 @@
                },


For clarity I'd write for both gtf and gff
"Either this parameter or gtf is mandatory if --genome is not specified."

bjlang · 2024-10-01T10:12:57Z

bin/check_samplesheet.py

+                            print_error(
+                                f"Control identifier and replicate has to match a provided sample identifier and replicate!",
+                                "Control",
+                                val[4],


Suggested change

val[4],

val[-1],

I believe val[5] should also be fine, but val[4] refers to the antibody

bjlang · 2024-10-01T10:16:39Z

README.md


 ## Credits

 These scripts were originally written by Chuan Wang ([@chuan-wang](https://github.com/chuan-wang)) and Phil Ewels ([@ewels](https://github.com/ewels)) for use at the [National Genomics Infrastructure](https://portal.scilifelab.se/genomics/) at [SciLifeLab](http://www.scilifelab.se/) in Stockholm, Sweden. The pipeline was re-implemented by Harshil Patel ([@drpatelh](https://github.com/drpatelh)) from [Seqera Labs, Spain](https://seqera.io/) and converted to Nextflow DSL2 by Jose Espinosa-Carrasco ([@JoseEspinosa](https://github.com/JoseEspinosa)) from [The Comparative Bioinformatics Group](https://www.crg.eu/en/cedric_notredame) at [The Centre for Genomic Regulation, Spain](https://www.crg.eu/).

-Many thanks to others who have helped out and contributed along the way too, including (but not limited to): [@apeltzer](https://github.com/apeltzer), [@bc2zb](https://github.com/bc2zb), [@crickbabs](https://github.com/crickbabs), [@drejom](https://github.com/drejom), [@houghtos](https://github.com/houghtos), [@KevinMenden](https://github.com/KevinMenden), [@mashehu](https://github.com/mashehu), [@pditommaso](https://github.com/pditommaso), [@Rotholandus](https://github.com/Rotholandus), [@sofiahaglund](https://github.com/sofiahaglund), [@tiagochst](https://github.com/tiagochst) and [@winni2k](https://github.com/winni2k).
+The pipeline workflow diagram was designe by Sarah Guinchard ([@G-Sarah](https://github.com/G-Sarah)).


Suggested change

The pipeline workflow diagram was designe by Sarah Guinchard ([@G-Sarah](https://github.com/G-Sarah)).

The pipeline workflow diagram was designed by Sarah Guinchard ([@G-Sarah](https://github.com/G-Sarah)).

bjlang · 2024-10-01T10:17:39Z

CHANGELOG.md

+| `multiqc`               | 1.13        | 1.23        |
+| `picard`                | 2.27.4      | 3.2.0       |
+| `samtools`              | 1.15.1      | 1.20        |
+| `samtools`              | 1.15.1      | 1.20        |


Suggested change

| `samtools` | 1.15.1 | 1.20 |

Duplicate line

bjlang · 2024-10-01T10:28:50Z

docs/usage.md


-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 perform the alignments in parallel, and subsequently merge them before further analysis. Below is an example where the samples called `WT_BCATENIN_IP_REP2` and `WT_INPUT_REP2` have been re-sequenced multiple times:
+The `sample` identifier should be identical when you have multiple replicates from the same experimental group, just increment the `replicate` identifier appropriately. The first replicate value for any given experimental group must be 1.


Suggested change

The `sample` identifier should be identical when you have multiple replicates from the same experimental group, just increment the `replicate` identifier appropriately. The first replicate value for any given experimental group must be 1.

The `sample` identifier should be identical when you have multiple replicates from the same experimental group; just increment the `replicate` identifier appropriately. The first replicate value for any given experimental group must be 1.

bjlang · 2024-10-01T10:30:00Z

docs/usage.md

@@ -143,29 +184,42 @@ nextflow pull nf-core/chipseq

 It is a good idea to specify a pipeline version when running the pipeline on your data. This ensures that a specific version of the pipeline code and software are used when you run your pipeline. If you keep using the same tag, you'll be running the same version of the pipeline, even if there have been changes to the code since.

-First, go to the [nf-core/chipseq releases page](https://github.com/nf-core/chipseq/releases) and find the latest version number - numeric only (eg. `1.2.2`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 1.2.2`.
+First, go to the [nf-core/chipseq releases page](https://github.com/nf-core/chipseq/releases) and find the latest pipeline version - numeric only (eg. `2.0.0`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 2.0.0`. Of course, you can switch to another version by changing the number after the `-r` flag.


Suggested change

First, go to the [nf-core/chipseq releases page](https://github.com/nf-core/chipseq/releases) and find the latest pipeline version - numeric only (eg. `2.0.0`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 2.0.0`. Of course, you can switch to another version by changing the number after the `-r` flag.

First, go to the [nf-core/chipseq releases page](https://github.com/nf-core/chipseq/releases) and find the latest pipeline version - numeric only (eg. `2.1.0`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 2.1.0`. Of course, you can switch to another version by changing the number after the `-r` flag.

workflows/chipseq.nf

bjlang · 2024-10-01T11:18:09Z

workflows/chipseq.nf

+ch_peak_count_header        = file("$projectDir/assets/multiqc/peak_count_header.txt", checkIfExists: true)
+ch_frip_score_header        = file("$projectDir/assets/multiqc/frip_score_header.txt", checkIfExists: true)
+ch_peak_annotation_header   = file("$projectDir/assets/multiqc/peak_annotation_header.txt", checkIfExists: true)
+ch_deseq2_pca_header        = Channel.value(file("$projectDir/assets/multiqc/deseq2_pca_header.txt", checkIfExists: true))


I can't spot a difference in the usage of this header vs e.g. the ch_peak_annotation_header. What's the reason for defining some as paths and some as value channels?

JoseEspinosa

I also missed in mine.....how do you do this? just direct commit to dev ?

I will open a small PR to dev instead, ping me if you need a review

Apply review suggestions

Fix how replicates are set for downstream analysis

JoseEspinosa added 30 commits April 18, 2023 16:01

Install custom/getchromsizes and picard/collectmultiplemetrics

28de291

Remove substituted modules and subworkflows

4c462b3

Rename bamtools/filter

3a33ed9

add align_star local subworkflow

0f70b6d

Refactor and rename bam_filter_bamtools

ccbc71c

Refactor code to use nf-core official subworkflows

0230090

Simplify code

3165a73

changelog

30312c3

Resolved arguments for bamtools_filteer

603db63

Update bowtie2/align to fix the container download

2637d88

Remove code used for view

6a75945

Feed missing arguments to star subworkflow

b00897d

Update chromap/chromap

be423bf

Update star_align

7cc3041

Update changelog

403a8e5

Update bowtie2/build

aece0fb

Merge pull request #339 from JoseEspinosa/fixes

3b94a84

Some fixes

Fix samplesheet control column in docs examples

0f4af2c

Try to clarify read_length docs

683428a

Fix macs_gsize help text

58bd1f6

Refine read_length help text

f4cbf2a

Update readme since the steps below mapping can be performed when chr…

23efb25

…omap is used with PE reads

Merge pull request #340 from JoseEspinosa/docs_fixes

51e86f4

Docs fixes

Update modules

eeb0198

Install bam_markduplicates_picard from nf-core repo

8daf956

Also update instances of bam_markduplicates_picard in modules

73919ee

Remove obsolet subworkflow

477491d

Fix bwa_index

6c32d4e

Update changelog

59c02c5

Make prettier happy

fa04941

JoseEspinosa added 4 commits September 30, 2024 12:20

Update phantompeakqualtools to remove oras

b2f68c7

Update version of image in output

3deb261

Bump version 2.1.0 of the pipeline

372e393

Merge pull request #415 from JoseEspinosa/updates

f47e8ed

Get rid of oras from module images

JoseEspinosa commented Sep 30, 2024

View reviewed changes

sateeshperi reviewed Sep 30, 2024

View reviewed changes

bjlang approved these changes Oct 1, 2024

View reviewed changes

JoseEspinosa commented Oct 1, 2024

View reviewed changes

sateeshperi approved these changes Oct 1, 2024

View reviewed changes

JoseEspinosa mentioned this pull request Oct 1, 2024

Refactor local modules to use an conda environment yml file and not ping modules directly #417

Open

JoseEspinosa added 7 commits October 1, 2024 16:15

Apply review sugestions on schema

0f18b62

Removed duplicated lines

e5c1a97

Fix tyop

bfcd696

Include DOI in nextflow.config

15a91e5

Correct index for printing error

a08fda9

Apply review suggestion

fcaeea4

Remove todo

b626b67

JoseEspinosa mentioned this pull request Oct 1, 2024

Apply review suggestions #418

Merged

3 tasks

JoseEspinosa added 11 commits October 1, 2024 22:15

Add release date

6998300

Add release credits

224ea8c

Add parameters to changelog

44a596c

Correct credits text

683728a

Fix output files rendering error (missing line)

b880175

Merge pull request #418 from JoseEspinosa/updates

dd37833

Apply review suggestions

Remove _REP from id for posterior grouping

0dc9408

Update changelog

75acca4

Fix changelog and update release date

5850c6c

Fix how groups are count

a950571

Merge pull request #420 from JoseEspinosa/updates

11ded3d

Fix how replicates are set for downstream analysis

JoseEspinosa merged commit 76e2382 into master Oct 7, 2024
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Dev -> Master for 2.1.0 release #413

Dev -> Master for 2.1.0 release #413

JoseEspinosa commented Sep 17, 2024

JoseEspinosa Sep 30, 2024

sateeshperi Oct 1, 2024

sateeshperi Sep 30, 2024

JoseEspinosa Oct 1, 2024

sateeshperi Sep 30, 2024

JoseEspinosa Oct 1, 2024

sateeshperi Sep 30, 2024

bjlang Sep 27, 2024

bjlang Oct 1, 2024

bjlang Oct 1, 2024

bjlang Oct 1, 2024

bjlang Oct 1, 2024

bjlang Oct 1, 2024

bjlang Oct 1, 2024

bjlang Oct 1, 2024

bjlang Oct 1, 2024

JoseEspinosa left a comment

	The pipeline workflow diagram was designe by Sarah Guinchard ([@G-Sarah](https://github.com/G-Sarah)).
	The pipeline workflow diagram was designed by Sarah Guinchard ([@G-Sarah](https://github.com/G-Sarah)).


		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 perform the alignments in parallel, and subsequently merge them before further analysis. Below is an example where the samples called `WT_BCATENIN_IP_REP2` and `WT_INPUT_REP2` have been re-sequenced multiple times:
		The `sample` identifier should be identical when you have multiple replicates from the same experimental group, just increment the `replicate` identifier appropriately. The first replicate value for any given experimental group must be 1.

	First, go to the [nf-core/chipseq releases page](https://github.com/nf-core/chipseq/releases) and find the latest pipeline version - numeric only (eg. `2.0.0`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 2.0.0`. Of course, you can switch to another version by changing the number after the `-r` flag.
	First, go to the [nf-core/chipseq releases page](https://github.com/nf-core/chipseq/releases) and find the latest pipeline version - numeric only (eg. `2.1.0`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 2.1.0`. Of course, you can switch to another version by changing the number after the `-r` flag.

Dev -> Master for 2.1.0 release #413

Dev -> Master for 2.1.0 release #413

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JoseEspinosa commented Sep 17, 2024

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