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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
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10 changed files with 63 additions and 19 deletions
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2
modules/cellranger/Dockerfile
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@ -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> # Push to nfcore/cellranger:<VER>
FROM continuumio/miniconda3:4.8.2 FROM continuumio/miniconda3:4.8.2

2
modules/cellranger/count/main.nf
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@ -5,7 +5,7 @@ process CELLRANGER_COUNT {
if (params.enable_conda) { if (params.enable_conda) {
exit 1, "Conda environments cannot be used when using the Cell Ranger tool. Please use docker or singularity containers." 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: input:
tuple val(meta), path(reads) tuple val(meta), path(reads)

4
modules/cellranger/mkfastq/Dockerfile
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@ -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> # Push to nfcore/cellrangermkfastq:<VER>
FROM continuumio/miniconda3:4.8.2 FROM continuumio/miniconda3:4.8.2
@ -17,7 +17,7 @@ RUN apt-get update --allow-releaseinfo-change \
# Copy pre-downloaded bcl2fastq2 and cellranger file # Copy pre-downloaded bcl2fastq2 and cellranger file
ENV BCL2FASTQ2_VER=v2-20-0-linux-x86-64 \ 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 bcl2fastq2-$BCL2FASTQ2_VER.zip /tmp/bcl2fastq2-$BCL2FASTQ2_VER.zip
COPY cellranger-$CELLRANGER_VER.tar.gz /opt/cellranger-$CELLRANGER_VER.tar.gz COPY cellranger-$CELLRANGER_VER.tar.gz /opt/cellranger-$CELLRANGER_VER.tar.gz

2
modules/cellranger/mkfastq/main.nf
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@ -5,7 +5,7 @@ process CELLRANGER_MKFASTQ {
if (params.enable_conda) { if (params.enable_conda) {
exit 1, "Conda environments cannot be used when using the Cell Ranger tool. Please use docker or singularity containers." 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: input:
path bcl path bcl

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

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

2
modules/cellranger/mkref/main.nf
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@ -5,7 +5,7 @@ process CELLRANGER_MKREF {
if (params.enable_conda) { if (params.enable_conda) {
exit 1, "Conda environments cannot be used when using the Cell Ranger tool. Please use docker or singularity containers." 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: input:
path fasta path fasta

56
tests/modules/cellranger/count/test.yml
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@ -1,19 +1,65 @@
- name: cellranger count test_cellranger_count - 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: tags:
- cellranger
- cellranger/count - cellranger/count
- cellranger
files: 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 - 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 - path: output/cellranger/sample-123/outs/metrics_summary.csv
md5sum: 707df0f101d479d93f412ca74f9c4131 md5sum: 707df0f101d479d93f412ca74f9c4131
- path: output/cellranger/sample-123/outs/molecule_info.h5 - path: output/cellranger/sample-123/outs/molecule_info.h5
md5sum: 0e56836ef0725f2ab05f56ca5a71e55b md5sum: a13bd7425f441c8d0eac8ffc50082996
- path: output/cellranger/sample-123/outs/possorted_genome_bam.bam - path: output/cellranger/sample-123/outs/possorted_genome_bam.bam
md5sum: 15441da9cfceea0bb48c8b66b1b860df md5sum: 15441da9cfceea0bb48c8b66b1b860df
- path: output/cellranger/sample-123/outs/possorted_genome_bam.bam.bai - path: output/cellranger/sample-123/outs/possorted_genome_bam.bam.bai
md5sum: 7c3d49c77016a09535aff61a027f750c md5sum: 7c3d49c77016a09535aff61a027f750c
- path: output/cellranger/sample-123/outs/raw_feature_bc_matrix
- path: output/cellranger/sample-123/outs/raw_feature_bc_matrix.h5 - 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 - 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 - cellranger/mkfastq
files: files:
- path: output/cellranger/cellranger-tiny-bcl-1/outs/fastq_path/fake_file.fastq.gz - path: output/cellranger/cellranger-tiny-bcl-1/outs/fastq_path/fake_file.fastq.gz
md5sum: d41d8cd98f00b204e9800998ecf8427e
- name: cellranger mkfastq test_cellranger_mkfastq_illumina - 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 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: tags:
@ -13,4 +12,3 @@
- cellranger/mkfastq - cellranger/mkfastq
files: files:
- path: output/cellranger/cellranger-tiny-bcl-1/outs/fastq_path/fake_file.fastq.gz - path: output/cellranger/cellranger-tiny-bcl-1/outs/fastq_path/fake_file.fastq.gz
md5sum: d41d8cd98f00b204e9800998ecf8427e

4
tests/modules/cellranger/mkgtf/test.yml
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@ -1,8 +1,8 @@
- name: cellranger mkgtf test_cellranger_mkgtf - 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: tags:
- cellranger
- cellranger/mkgtf - cellranger/mkgtf
- cellranger
files: files:
- path: output/cellranger/genome.filtered.gtf - path: output/cellranger/genome.filtered.gtf
md5sum: a8b8a7b5039e05d3a9cf9151ea138b5b md5sum: a8b8a7b5039e05d3a9cf9151ea138b5b

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