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Merge pull request #1751 from nf-core/cellranger-7.0.0

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CellRanger 7.0.0 / Apart from cconda, all is green 🥳
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Alexander Peltzer 2022-06-10 12:02:30 +02:00 committed by GitHub
commit f7b2314ec4
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10 changed files with 63 additions and 19 deletions
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2
modules/cellranger/Dockerfile
View file

@ -1,4 +1,4 @@
# Dockerfile to create container with Cell Ranger v6.1.2
# Dockerfile to create container with Cell Ranger v7.0.0
# Push to nfcore/cellranger:<VER>
FROM continuumio/miniconda3:4.8.2

2
modules/cellranger/count/main.nf
View file

@ -5,7 +5,7 @@ process CELLRANGER_COUNT {
if (params.enable_conda) {
exit 1, "Conda environments cannot be used when using the Cell Ranger tool. Please use docker or singularity containers."
}
container "nfcore/cellranger:6.1.2"
container "nfcore/cellranger:7.0.0"
input:
tuple val(meta), path(reads)

4
modules/cellranger/mkfastq/Dockerfile
View file

@ -1,4 +1,4 @@
# Dockerfile to create container with Cell Ranger v6.1.2 and bcl2fastq v2.20.0
# Dockerfile to create container with Cell Ranger v7.0.0 and bcl2fastq v2.20.0
# Push to nfcore/cellrangermkfastq:<VER>
FROM continuumio/miniconda3:4.8.2
@ -17,7 +17,7 @@ RUN apt-get update --allow-releaseinfo-change \
# Copy pre-downloaded bcl2fastq2 and cellranger file
ENV BCL2FASTQ2_VER=v2-20-0-linux-x86-64 \
CELLRANGER_VER=6.1.2
CELLRANGER_VER=7.0.0
COPY bcl2fastq2-$BCL2FASTQ2_VER.zip /tmp/bcl2fastq2-$BCL2FASTQ2_VER.zip
COPY cellranger-$CELLRANGER_VER.tar.gz /opt/cellranger-$CELLRANGER_VER.tar.gz

2
modules/cellranger/mkfastq/main.nf
View file

@ -5,7 +5,7 @@ process CELLRANGER_MKFASTQ {
if (params.enable_conda) {
exit 1, "Conda environments cannot be used when using the Cell Ranger tool. Please use docker or singularity containers."
}
container "nfcore/cellrangermkfastq:6.1.2"
container "nfcore/cellrangermkfastq:7.0.0"
input:
path bcl

2
modules/cellranger/mkgtf/main.nf
View file

@ -5,7 +5,7 @@ process CELLRANGER_MKGTF {
if (params.enable_conda) {
exit 1, "Conda environments cannot be used when using the Cell Ranger tool. Please use docker or singularity containers."
}
container "nfcore/cellranger:6.1.2"
container "nfcore/cellranger:7.0.0"
input:
path gtf

2
modules/cellranger/mkref/main.nf
View file

@ -5,7 +5,7 @@ process CELLRANGER_MKREF {
if (params.enable_conda) {
exit 1, "Conda environments cannot be used when using the Cell Ranger tool. Please use docker or singularity containers."
}
container "nfcore/cellranger:6.1.2"
container "nfcore/cellranger:7.0.0"
input:
path fasta

56
tests/modules/cellranger/count/test.yml
View file

@ -1,19 +1,65 @@
- name: cellranger count test_cellranger_count
command: nextflow run tests/modules/cellranger/count -entry test_cellranger_count -c tests/config/nextflow.config -c tests/modules/cellranger/count/nextflow.config
command: nextflow run ./tests/modules/cellranger/count -entry test_cellranger_count -c ./tests/config/nextflow.config -c ./tests/modules/cellranger/count/nextflow.config
tags:
- cellranger
- cellranger/count
- cellranger
files:
- path: output/cellranger/genome.filtered.gtf
md5sum: a8b8a7b5039e05d3a9cf9151ea138b5b
- path: output/cellranger/homo_sapiens_chr22_reference/fasta/genome.fa
md5sum: f315020d899597c1b57e5fe9f60f4c3e
- path: output/cellranger/homo_sapiens_chr22_reference/fasta/genome.fa.fai
md5sum: 3520cd30e1b100e55f578db9c855f685
- path: output/cellranger/homo_sapiens_chr22_reference/genes/genes.gtf.gz
md5sum: d1e05cd46684fa26d852b6bc9f05e31f
- path: output/cellranger/homo_sapiens_chr22_reference/reference.json
md5sum: 8405fd7f527a944eafb9c2909045840b
- path: output/cellranger/homo_sapiens_chr22_reference/star/Genome
md5sum: 897cec2d191945335f8b320438bd9135
- path: output/cellranger/homo_sapiens_chr22_reference/star/SA
md5sum: 7961129ac5d0e1706105be1d31c6b30c
- path: output/cellranger/homo_sapiens_chr22_reference/star/SAindex
md5sum: dcceb480b30cda93fb8c63ddc339093b
- path: output/cellranger/homo_sapiens_chr22_reference/star/chrLength.txt
md5sum: c81f40f27e72606d7d07097c1d56a5b5
- path: output/cellranger/homo_sapiens_chr22_reference/star/chrName.txt
md5sum: 5ae68a67b70976ee95342a7451cb5af1
- path: output/cellranger/homo_sapiens_chr22_reference/star/chrNameLength.txt
md5sum: b190587cae0531f3cf25552d8aa674db
- path: output/cellranger/homo_sapiens_chr22_reference/star/chrStart.txt
md5sum: bc73df776dd3d5bb9cfcbcba60880519
- path: output/cellranger/homo_sapiens_chr22_reference/star/exonGeTrInfo.tab
md5sum: 9129691eeb4ed0d02b17be879fa3edb0
- path: output/cellranger/homo_sapiens_chr22_reference/star/exonInfo.tab
md5sum: 209b82f0683efd03e17d2c729676554f
- path: output/cellranger/homo_sapiens_chr22_reference/star/geneInfo.tab
md5sum: 02a8f4575bdfcd4a42b4d8d07f2e9369
- path: output/cellranger/homo_sapiens_chr22_reference/star/genomeParameters.txt
- path: output/cellranger/homo_sapiens_chr22_reference/star/sjdbInfo.txt
md5sum: 1082ab459363b3f2f7aabcef0979c1ed
- path: output/cellranger/homo_sapiens_chr22_reference/star/sjdbList.fromGTF.out.tab
- path: output/cellranger/homo_sapiens_chr22_reference/star/sjdbList.out.tab
- path: output/cellranger/homo_sapiens_chr22_reference/star/transcriptInfo.tab
md5sum: cedcb5f4e7d97bc548cd5daa022e092c
- path: output/cellranger/sample-123/outs/filtered_feature_bc_matrix.h5
md5sum: f8b6b7cc8248151a98c46d4ebec450c6
- path: output/cellranger/sample-123/outs/filtered_feature_bc_matrix/barcodes.tsv.gz
- path: output/cellranger/sample-123/outs/filtered_feature_bc_matrix/features.tsv.gz
- path: output/cellranger/sample-123/outs/filtered_feature_bc_matrix/matrix.mtx.gz
- path: output/cellranger/sample-123/outs/metrics_summary.csv
md5sum: 707df0f101d479d93f412ca74f9c4131
- path: output/cellranger/sample-123/outs/molecule_info.h5
md5sum: 0e56836ef0725f2ab05f56ca5a71e55b
md5sum: a13bd7425f441c8d0eac8ffc50082996
- path: output/cellranger/sample-123/outs/possorted_genome_bam.bam
md5sum: 15441da9cfceea0bb48c8b66b1b860df
- path: output/cellranger/sample-123/outs/possorted_genome_bam.bam.bai
md5sum: 7c3d49c77016a09535aff61a027f750c
- path: output/cellranger/sample-123/outs/raw_feature_bc_matrix
- path: output/cellranger/sample-123/outs/raw_feature_bc_matrix.h5
md5sum: cdad1cd7b215d7137cf92515e81a8525
md5sum: a5290f3e300a4070f3d68a0c2e215f54
- path: output/cellranger/sample-123/outs/raw_feature_bc_matrix/barcodes.tsv.gz
md5sum: 5cc39ef0c7ac85f2b758b164aabf9157
- path: output/cellranger/sample-123/outs/raw_feature_bc_matrix/features.tsv.gz
md5sum: 07d497c7ce3e22f374af7b2cf9b97d72
- path: output/cellranger/sample-123/outs/raw_feature_bc_matrix/matrix.mtx.gz
md5sum: bdce94a51f16e22d40301724080b76ee
- path: output/cellranger/sample-123/outs/web_summary.html

2
tests/modules/cellranger/mkfastq/test.yml
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@ -5,7 +5,6 @@
- cellranger/mkfastq
files:
- path: output/cellranger/cellranger-tiny-bcl-1/outs/fastq_path/fake_file.fastq.gz
md5sum: d41d8cd98f00b204e9800998ecf8427e
- name: cellranger mkfastq test_cellranger_mkfastq_illumina
command: nextflow run tests/modules/cellranger/mkfastq -entry test_cellranger_mkfastq_illumina -c tests/config/nextflow.config -c ./tests/modules/cellranger/mkfastq/nextflow.config -stub-run
tags:
@ -13,4 +12,3 @@
- cellranger/mkfastq
files:
- path: output/cellranger/cellranger-tiny-bcl-1/outs/fastq_path/fake_file.fastq.gz
md5sum: d41d8cd98f00b204e9800998ecf8427e

4
tests/modules/cellranger/mkgtf/test.yml
View file

@ -1,8 +1,8 @@
- name: cellranger mkgtf test_cellranger_mkgtf
command: nextflow run tests/modules/cellranger/mkgtf -entry test_cellranger_mkgtf -c tests/config/nextflow.config -c tests/modules/cellranger/mkgtf/nextflow.config
command: nextflow run ./tests/modules/cellranger/mkgtf -entry test_cellranger_mkgtf -c ./tests/config/nextflow.config -c ./tests/modules/cellranger/mkgtf/nextflow.config
tags:
- cellranger
- cellranger/mkgtf
- cellranger
files:
- path: output/cellranger/genome.filtered.gtf
md5sum: a8b8a7b5039e05d3a9cf9151ea138b5b

4
tests/modules/cellranger/mkref/test.yml
View file

@ -1,8 +1,8 @@
- name: cellranger mkref test_cellranger_mkref
command: nextflow run ./tests/modules/cellranger/mkref -entry test_cellranger_mkref -c ./tests/config/nextflow.config -c ./tests/modules/cellranger/mkref/nextflow.config
tags:
- cellranger
- cellranger/mkref
- cellranger
files:
- path: output/cellranger/homo_sapiens_chr22_reference/fasta/genome.fa
md5sum: f315020d899597c1b57e5fe9f60f4c3e
@ -11,7 +11,7 @@
- path: output/cellranger/homo_sapiens_chr22_reference/genes/genes.gtf.gz
md5sum: 6d9b5f409bfea95022bc25b9590e194e
- path: output/cellranger/homo_sapiens_chr22_reference/reference.json
md5sum: 5d8d1669cd251433505f183e1c9ed6bc
md5sum: 6cc817f0923062e780e6573806840cea
- path: output/cellranger/homo_sapiens_chr22_reference/star/Genome
md5sum: 22102926fadf5890e905ca71b2da3f35
- path: output/cellranger/homo_sapiens_chr22_reference/star/SA