Merge branch 'v1.6' into main

wtsi-hgi · Jun 12, 2024 · 6fc3e91 · 6fc3e91
2 parents 4923729 + ac9e8c6
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diff --git a/README.md b/README.md
@@ -4,7 +4,7 @@
 
 ## Introduction
 
-**nf-core/yascp** is a bioinformatics best-practice analysis pipeline tailored for deconvolution, quality control, clustering, and integration of single-cell datasets. Developed under the leadership of N.Soranzo and Human Genetics Informatics (HGI), this large-scale single-cell pipeline was originally crafted for the Cardinal project (profiling UKBB and ELGH participants) but is versatile enough for broader scRNA analysis applications. The foundational ideas were inspired by earlier pipelines from Anderson lab but has been expanded, specifically those for [deconvolution](https://github.com/wtsi-hgi/nf_scrna_deconvolution.git), [cellbender](https://github.com/wtsi-hgi/nf_cellbender), and [quality control and clustering](https://github.com/wtsi-hgi/nf_qc_cluster/tree/main). This ensures a robust integration of proven methodologies tailored to meet the demands of expansive single-cell data analysis.
+**nf-core/yascp** is a bioinformatics best-practice analysis pipeline tailored for deconvolution, quality control, clustering, and integration of single-cell datasets. Developed under the leadership of N.Soranzo and Human Genetics Informatics (HGI), this large-scale single-cell pipeline was originally crafted for the Cardinal project (profiling UKBB and ELGH participants) but is versatile enough for broader scRNA analysis applications and has had contributions from many other teams across Sanger. The foundational ideas were inspired by earlier pipelines from Anderson lab that have been significantly expanded and improved - specifically those for [deconvolution](https://github.com/wtsi-hgi/nf_scrna_deconvolution.git), [cellbender](https://github.com/wtsi-hgi/nf_cellbender), and [quality control and clustering](https://github.com/wtsi-hgi/nf_qc_cluster/tree/main). This ensures a robust integration of proven methodologies tailored to meet the demands of expansive single-cell data analysis.
 
 Input requires a tsv seperated file [(please read detailed documentation here)](https://github.com/wtsi-hgi/yascp/tree/yascp_docs) with paths and if running in an genotype  additional input is required to be provided in an input.nf file pointing to the vcf location. This pipeline is designed to be used any large scale single cell experiments.
 
@@ -71,7 +71,7 @@ Easyest to do is using a conda enviroment.
 
 ## Credits
 
-Yascp was originally written by Matiss Ozols as part of the Cardinal project but is applicable to many other projects with contributions from Leland Taylor, Guillaume Noell, Hannes Ponstingl, Vivek Iyer,  Henry Taylor, Tobi Alegbe, Monika Krzak, Alessandro Raveane, Carl Anderson, Anna Lorenc, Stephen Watt, Nicole Soranzo.
+Yascp was originally written by Matiss Ozols as part of the Cardinal project but is applicable to many other projects with contributions from Leland Taylor, Guillaume Noell, Hannes Ponstingl, Vivek Iyer,  Henry Taylor, Tobi Alegbe, Monika Krzak, Alessandro Raveane, Carl Anderson, Anna Lorenc, Haerin Jang, Niek de Klein, Stephen Watt, Nicole Soranzo.
 <!-- TODO nf-core: If applicable, make list of people who have also contributed -->
 
 The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!

diff --git a/assets/deploy_scripts/module_exacutables/help.info b/assets/deploy_scripts/module_exacutables/help.info
@@ -3,6 +3,7 @@
 ###################
 ${bold}YASCP (Yet Another Single Cell Pieline)${normal}[https://github.com/wtsi-hgi/yascp]
 Nextflow pipeline that QCs the scRNA Cellranger data by removing ambient RNA, deconvoluting donors, assigning celltypes, analysing concordances vs expected genotypes
+Please refear to the usage and outputs documentation here: https://hgi-projects.pages.internal.sanger.ac.uk/documentation/docs/tutorials/yascp_docs/#getting-started or here: https://github.com/wtsi-hgi/yascp/tree/78df9d94388045bc386ea32c2127abeb154a36c6 
 ###################
 
 Yascp module has been set to run in multiple modes:

diff --git a/assets/deploy_scripts/module_exacutables/yascp b/assets/deploy_scripts/module_exacutables/yascp
@@ -5,6 +5,7 @@ bold=$(tput bold)
 normal=$(tput sgr0)
 
 
+
 if [[ "$QUEUE" == '' ]];
     then
         export QUEUE='long'

diff --git a/assets/deploy_scripts/sanger_module_files/1.6 b/assets/deploy_scripts/sanger_module_files/1.6
@@ -33,7 +33,7 @@ module load ISG/singularity/3.11.4
 module load HGI/common/nextflow/22.04.4
 module load HGI/common/baton
 module load ISG/experimental/irods/4.2.7
-
+module load HGI/softpack/users/bh18/bcftools/1.0
 prepend-path PATH "/software/hgi/envs/conda/team151/mo11/mo11/bin"
 prepend-path PATH "/software/hgi/containers/yascp/modules/full_yascp"
 prepend-path PATH "/software/hgi/pipelines/yascp_versions/yascp_v1.6/bin"