I think it's --steps not --step

Update metro map

Fix typo in nextflow_schema.json

* Use cram file

* Update conf

* Add sbwf bam check chr

* Rehead bam file with awk

* Move samtools merge to bam region

* Fix config file

* Fix name imputation

* Fix test cram bam

* Remove process for samples and only publish once panel

* Rename process

* Add renaming and check sbwf for bam

* Simplify contig check

* Rename workflow

* Rename test

* Improve nf-test

* Add workflow and metro map

* Fix check contig names

* Add check chr workflow to phaseimpute and improve it

* Add nextflow schema to nf-test config

* Add nf-test to initialisation pipeline

* Patch modules

* Fix nf-test

* Update CHANGELOG

* Fix empty chr channel

* Fix file prefix

* Fix file prefix

* Fix samplesheet column name

* Fix fai combination

* Update CHANGELOG

* Improve Glimpse2 phasing process

* Add example

* Remove input_region for full chromosome

* Improve comment

* Update subworkflows/local/vcf_normalize_bcftools/main.nf

Co-authored-by: Anabella Trigila <[email protected]>

* Update workflows/phaseimpute/main.nf

Co-authored-by: Anabella Trigila <[email protected]>

* Rename modules

* Rename function

* Use ch_chr as channel for CHECKCHR

* Improve output naming after simulation

* Improve sbwf and channel names

* Fix sbwf name

* Fall back to lst_chr

* Patch glimpse2 phase

* Move to 23.10.0

* Update snap

* Update snapshot

* Rename full conf

* Simplify check chr in initialisation

* Simplify chr renaming channel manipulation

* Fix function

* Improve chrcheck and add documentation

* Explain format usage for input samplesheet

* Relocate function chrcheck

* Update CHANGELOG.md

Co-authored-by: Maxime U Garcia <[email protected]>

* Update conf/test_all_fullchr.config

Co-authored-by: Maxime U Garcia <[email protected]>

* Remove temporary draw io file

* Pin hstlib

* Fix sbwf naming

* Add checkFileIndex

* Fix channel name

---------

Co-authored-by: LouisLeNezet <[email protected]>
Co-authored-by: Anabella Trigila <[email protected]>
Co-authored-by: Maxime U Garcia <[email protected]>

* Rename sbwf to bam_

* Update Mpileup

* Patch gawk

* Use legend file for posfile and simplify usage

* Rename gmap output

* Gawk now support list of gz files

* Remove csv sbwf

* Add csv export function and nf-test it

* Update documentation and CHANGELOG

* Patch bcftools mpileup

* Update Readme

* Update to ext.args2 for GAWK

* Modify error message for legend

* Improve documentation

* Improve documentation

* Create different posfile samplesheet to test minimal requirement

* Update docs/usage.md

Co-authored-by: Anabella Trigila <[email protected]>

* Update documentation

* Delete requirement from posfile asset

* Remove view

* Add optional tools to meta

* Rename to exportCsv

* Update file format usage

* Move exportCsv to utils

* Remove empty channel test as not working

* Fix disjoint

* Fix sbwf naming

* Move test to utils

* Remove chr:null

* Fix arity of gawk

* Fix for no chr in list

* Simplify posfile usage

* Delete print

* Fix checkFileIndex

* Do not publish chrcheck

* Fix gawk arity

* Fix sbw config name

* Update snapshot

* Add log

* Add log

* Add log

* Remove log

---------

Co-authored-by: LouisLeNezet <[email protected]>
Co-authored-by: Anabella Trigila <[email protected]>

* Change compute_freq default to false

* Update Changelog

* Update Bcftools annotate

* Update Bcftools concat

* Update Bcftools convert

* Update Bcftools index

* Update Bcftools norm

* Update bcftools pluginsplit

* Remove unused bcftools query

* Update bcftools view

* Update dumpsoftwareversions

* Update Gawk

* Update glimpse2 chunk

* Update glimpse2 concordance

* Update glimpse2 ligate splitreference

* Update glimpse2 phase

* Update Gunzip

* Update multiqc

* Update samtools faidx

* Update samtools merge

* Update samtools index

* Update samtools reheader

* Update samtools view

* Update modules.json

* Patch samtools view

* Update bcftools

* Patch bcftools concat

* Fix getfilesextension for null file, add debug and fix variable

* Update gawk

* Fix samtools index

* Update changelog

* Remove uncessary process

* Fix chunking

* Update snapshot

* Update snapshot

* Update snapshot

* Update checkFileIndex function to collect the file before checking

---------

Co-authored-by: LouisLeNezet <[email protected]>

* Compute chr list from vcf not from whole file

* Update all nf-core modules (#100)

* Update Bcftools annotate

* Update Bcftools concat

* Update Bcftools convert

* Update Bcftools index

* Update Bcftools norm

* Update bcftools pluginsplit

* Remove unused bcftools query

* Update bcftools view

* Update dumpsoftwareversions

* Update Gawk

* Update glimpse2 chunk

* Update glimpse2 concordance

* Update glimpse2 ligate splitreference

* Update glimpse2 phase

* Update Gunzip

* Update multiqc

* Update samtools faidx

* Update samtools merge

* Update samtools index

* Update samtools reheader

* Update samtools view

* Update modules.json

* Patch samtools view

* Update bcftools

* Patch bcftools concat

* Fix getfilesextension for null file, add debug and fix variable

* Update gawk

* Fix samtools index

* Update changelog

* Remove uncessary process

* Fix chunking

* Update snapshot

* Update snapshot

* Update snapshot

* Update checkFileIndex function to collect the file before checking

---------

Co-authored-by: LouisLeNezet <[email protected]>

* Update getFileExtension

* Fix checkFileIndex

* Set ch_regions as intersect of contigs, add test and documentation

* Add more comment

* Add test for checkFileIndex

* remove unused subworkflow (#105)

* Update data tests sets

* Update Quilt sbwf, fix checkFileIndex, update snapshot

* Update snapshot and function test

* Add dog test

* Update subworkflows/local/utils_nfcore_phaseimpute_pipeline/tests/function.nf.test

Co-authored-by: Anabella Trigila <[email protected]>

* Add more test to vcf_chr_rename

---------

Co-authored-by: LouisLeNezet <[email protected]>
Co-authored-by: Anabella Trigila <[email protected]>

* Update glimpse2 phase to nf-core

* Update gunzip

* Update multiqc

* Update changelog

* remove unused subworkflow (#105)

* Fix chr name errors (#102)

* Compute chr list from vcf not from whole file

* Update all nf-core modules (#100)

* Update Bcftools annotate

* Update Bcftools concat

* Update Bcftools convert

* Update Bcftools index

* Update Bcftools norm

* Update bcftools pluginsplit

* Remove unused bcftools query

* Update bcftools view

* Update dumpsoftwareversions

* Update Gawk

* Update glimpse2 chunk

* Update glimpse2 concordance

* Update glimpse2 ligate splitreference

* Update glimpse2 phase

* Update Gunzip

* Update multiqc

* Update samtools faidx

* Update samtools merge

* Update samtools index

* Update samtools reheader

* Update samtools view

* Update modules.json

* Patch samtools view

* Update bcftools

* Patch bcftools concat

* Fix getfilesextension for null file, add debug and fix variable

* Update gawk

* Fix samtools index

* Update changelog

* Remove uncessary process

* Fix chunking

* Update snapshot

* Update snapshot

* Update snapshot

* Update checkFileIndex function to collect the file before checking

---------

Co-authored-by: LouisLeNezet <[email protected]>

* Update getFileExtension

* Fix checkFileIndex

* Set ch_regions as intersect of contigs, add test and documentation

* Add more comment

* Add test for checkFileIndex

* remove unused subworkflow (#105)

* Update data tests sets

* Update Quilt sbwf, fix checkFileIndex, update snapshot

* Update snapshot and function test

* Add dog test

* Update subworkflows/local/utils_nfcore_phaseimpute_pipeline/tests/function.nf.test

Co-authored-by: Anabella Trigila <[email protected]>

* Add more test to vcf_chr_rename

---------

Co-authored-by: LouisLeNezet <[email protected]>
Co-authored-by: Anabella Trigila <[email protected]>

---------

Co-authored-by: LouisLeNezet <[email protected]>
Co-authored-by: Anabella Trigila <[email protected]>

* Update sample sim full

* Fix path to full sample

* Add nft-vcf

* Add new nf-test for local sbwf and modules

* Add other nf-test

* Add new nf-tests

* Improve tests

* Patch bcftools merge

* Update changelog and delete .view()

* Delete .view()

* Update test_all

* Add assertions

---------

Co-authored-by: LouisLeNezet <[email protected]>

Co-authored-by: Louis LE NEZET <[email protected]>

Improve tests in dog genome

change output directory

* Template update for nf-core/tools version 3.0.0

* Template update for nf-core/tools version 3.0.1

* Update template_version_comment.yml

* Update template_version_comment.yml

* Add title to usage files

* Remove old way igenomes config

* Update main.nf and utils nf-core sbwf

* Update schema json

* Fix linting

* Update validation snap

---------

Co-authored-by: nf-core-bot <[email protected]>

* Template update for nf-core/tools version 3.0.0

* Template update for nf-core/tools version 3.0.1

* Template update for nf-core/tools version 3.0.2

* Update sha

---------

Co-authored-by: Louis Le Nezet <[email protected]>

* New dev

* Rename function

* Fix function

* Update workflow name

* Update tests

* Update function usage

* Update tests snapshot

* Update changelog

* Change phased to phase

* Update documentation

* Update snapshot

* Update publishing panel

* Update test

* Update docs/usage.md

Co-authored-by: Anabella Trigila <[email protected]>

---------

Co-authored-by: Anabella Trigila <[email protected]>

* Update workflow metro map

* Update metro map

* Update metro map and add animation

* Improve timing svg

* Update README.md

---------

Co-authored-by: LouisLeNezet <[email protected]>

* Remove phase autodetect

* Aggregate glimpse1 bams, merge vcf

* Aggregate glimpse and quilt bams

* Add to conf

* Add fasta to quilt and keep vcf merged

* Add modules list_to_file

* Order called sample

* Take out GL computation from swf glimpse1

* Add bamlist to quilt and glimpse2

* Put stitch parameters preparation in stitch sbwf

* Add batch_size and group samples in main workflow

* Update config

* Update config

* Add validation of batch size and tools compatibility

* Update test workflow

* Add batch to metamap

* Update conf

* Fix bam regions map

* Use dot as separator

* Update test and Changelog

* Update docs

* Improve documentation

* Patch modified modules

* Order samples names in snaphot

* Update changelog

* Improve pipeline

* Order files before grouping and split output vcf

* Add validation to snapshot

* Update schema description

* Fix tags

* Add splitting by samples for each output

* Split validation truth set by sample

* Fix split

* Put in samples folder

---------

Co-authored-by: LouisLeNezet <[email protected]>

* Update bcftools annotate

* Update bcftools concat

* Update bcftools convert

* Update bcftools index

* Update bcftools merge

* Update bcftools mpileup

* Update bcftools norm

* Update bcftools pluginsplit

* Update bcftools stats

* Update bcftools view

* Update bedtools makewindows

* Remove dumpsoftware

* Update gawk

* Update glimpse

* Update glimpse2

* Update gunzip

* Update quilt

* Update samtools

* Update shapeit5

* Update shapeit5

* Update stitch

* Update tabix

* Update vcflib

* Fix linting

* Update pluginsplit

* typo fixes in readme

* remove some to-dos

* remove todos, add bibliography

* add conditional detection of tools

* add missing tools to citations

* add conditional params

* add release name and date

* bump versions

* add contributors and reviewers

* Update README.md

* Update README.md

* Update README.md

---------

Co-authored-by: Louis LE NEZET <[email protected]>

Fix checkchr

* Remove conda from PR test

* Add seed for stitch and quilt

* Bump version in nf-core yml

* Update changelog

* updates in the README and usage files

* updated README file

* documents after prettier

* lastest update in usage file

* Conda check removed and seed parameters added for QUILT (#146)

* Remove conda from PR test

* Add seed for stitch and quilt

* Bump version in nf-core yml

* Update changelog

* updates in the README and usage files

* Fix linting

* CHANGELOG prettier

* alteration added to the Changed section

---------

Co-authored-by: Louis LE NEZET <[email protected]>

Replacing "./" from usage file.

* Fix workflow dispatch

* Remove TODO

* Remove map

* Fix gstring error

* Update Changelog

* Update Changelog

* Update readme

* Fix url link

* Fix url link in output

* Fix url link in output

* Fix url link in citation

* Add space to badges

* Update CHANGELOG

* Add white background to images

* Update Changelog