From e36b79201df4f21e4657b08b4e85a2ca68c612f3 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Fri, 10 Jun 2022 10:52:13 +0200 Subject: [PATCH 01/11] Update Dockerfile --- modules/cellranger/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/cellranger/Dockerfile b/modules/cellranger/Dockerfile index 3e52ca6a..266a24ef 100644 --- a/modules/cellranger/Dockerfile +++ b/modules/cellranger/Dockerfile @@ -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: FROM continuumio/miniconda3:4.8.2 From 8032833e6e0fd3edeb20d4121885112249f273c4 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Fri, 10 Jun 2022 10:53:09 +0200 Subject: [PATCH 02/11] Update main.nf --- modules/cellranger/count/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/cellranger/count/main.nf b/modules/cellranger/count/main.nf index 6a206b6e..7413c990 100644 --- a/modules/cellranger/count/main.nf +++ b/modules/cellranger/count/main.nf @@ -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) From e499abe572bc7c1322dfa66b767b0e65fe8c62ca Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Fri, 10 Jun 2022 10:53:48 +0200 Subject: [PATCH 03/11] Update main.nf --- modules/cellranger/mkgtf/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/cellranger/mkgtf/main.nf b/modules/cellranger/mkgtf/main.nf index 9dc2fe1a..a115706d 100644 --- a/modules/cellranger/mkgtf/main.nf +++ b/modules/cellranger/mkgtf/main.nf @@ -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 From 61d87bb2bcbcd058e1af6e5f14bb821b8ae4ed3e Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Fri, 10 Jun 2022 10:54:06 +0200 Subject: [PATCH 04/11] Update main.nf --- modules/cellranger/mkref/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/cellranger/mkref/main.nf b/modules/cellranger/mkref/main.nf index 11cf80e3..e1bfebde 100644 --- a/modules/cellranger/mkref/main.nf +++ b/modules/cellranger/mkref/main.nf @@ -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 From cfcd93f3e78b1c7e7490b702be8a5fadb8a55d2d Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Fri, 10 Jun 2022 10:56:13 +0200 Subject: [PATCH 05/11] Update Dockerfile --- modules/cellranger/mkfastq/Dockerfile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/cellranger/mkfastq/Dockerfile b/modules/cellranger/mkfastq/Dockerfile index 8660293a..7b6b84ec 100644 --- a/modules/cellranger/mkfastq/Dockerfile +++ b/modules/cellranger/mkfastq/Dockerfile @@ -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: 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 From 62c4b59d100d36488323041ac1a9e88b392eba36 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Fri, 10 Jun 2022 11:05:59 +0200 Subject: [PATCH 06/11] Update main.nf --- modules/cellranger/mkfastq/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/cellranger/mkfastq/main.nf b/modules/cellranger/mkfastq/main.nf index 9c023bca..30c638ea 100644 --- a/modules/cellranger/mkfastq/main.nf +++ b/modules/cellranger/mkfastq/main.nf @@ -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 From 570a43ba4c2b3b632662ded334002bd528365382 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Fri, 10 Jun 2022 11:21:03 +0200 Subject: [PATCH 07/11] Fix tests --- tests/modules/cellranger/count/test.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/modules/cellranger/count/test.yml b/tests/modules/cellranger/count/test.yml index 121d9eea..e29baaf0 100644 --- a/tests/modules/cellranger/count/test.yml +++ b/tests/modules/cellranger/count/test.yml @@ -8,12 +8,12 @@ - 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/web_summary.html From 4928dfad345f7b2a3a045140b95ea5a9f0a99e9e Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Fri, 10 Jun 2022 11:22:45 +0200 Subject: [PATCH 08/11] Trying to fix tests --- tests/modules/cellranger/mkref/test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/modules/cellranger/mkref/test.yml b/tests/modules/cellranger/mkref/test.yml index e40592bb..3f63b59c 100644 --- a/tests/modules/cellranger/mkref/test.yml +++ b/tests/modules/cellranger/mkref/test.yml @@ -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 From 1fbe69cfcc13ab98ee20c7eb6fdb3aaac420a9d0 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Fri, 10 Jun 2022 11:46:23 +0200 Subject: [PATCH 09/11] Updated and fixed tests --- tests/modules/cellranger/count/test.yml | 54 +++++++++++++++++++++++-- tests/modules/cellranger/mkgtf/test.yml | 4 +- tests/modules/cellranger/mkref/test.yml | 4 +- 3 files changed, 55 insertions(+), 7 deletions(-) diff --git a/tests/modules/cellranger/count/test.yml b/tests/modules/cellranger/count/test.yml index e29baaf0..2f49daf5 100644 --- a/tests/modules/cellranger/count/test.yml +++ b/tests/modules/cellranger/count/test.yml @@ -1,10 +1,53 @@ - 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 + md5sum: d41d8cd98f00b204e9800998ecf8427e + - path: output/cellranger/homo_sapiens_chr22_reference/star/sjdbList.out.tab + md5sum: d41d8cd98f00b204e9800998ecf8427e + - 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 @@ -13,7 +56,12 @@ 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: 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 diff --git a/tests/modules/cellranger/mkgtf/test.yml b/tests/modules/cellranger/mkgtf/test.yml index 2130afd2..59eb9072 100644 --- a/tests/modules/cellranger/mkgtf/test.yml +++ b/tests/modules/cellranger/mkgtf/test.yml @@ -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 diff --git a/tests/modules/cellranger/mkref/test.yml b/tests/modules/cellranger/mkref/test.yml index 3f63b59c..83ec5f95 100644 --- a/tests/modules/cellranger/mkref/test.yml +++ b/tests/modules/cellranger/mkref/test.yml @@ -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 + 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 From 63f47551a84741e7f495e8b381788ae13efb3ec6 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Fri, 10 Jun 2022 11:52:30 +0200 Subject: [PATCH 10/11] Fix empty test having md5sum --- tests/modules/cellranger/count/test.yml | 2 -- 1 file changed, 2 deletions(-) diff --git a/tests/modules/cellranger/count/test.yml b/tests/modules/cellranger/count/test.yml index 2f49daf5..93e52c4a 100644 --- a/tests/modules/cellranger/count/test.yml +++ b/tests/modules/cellranger/count/test.yml @@ -38,9 +38,7 @@ - path: output/cellranger/homo_sapiens_chr22_reference/star/sjdbInfo.txt md5sum: 1082ab459363b3f2f7aabcef0979c1ed - path: output/cellranger/homo_sapiens_chr22_reference/star/sjdbList.fromGTF.out.tab - md5sum: d41d8cd98f00b204e9800998ecf8427e - path: output/cellranger/homo_sapiens_chr22_reference/star/sjdbList.out.tab - md5sum: d41d8cd98f00b204e9800998ecf8427e - path: output/cellranger/homo_sapiens_chr22_reference/star/transcriptInfo.tab md5sum: cedcb5f4e7d97bc548cd5daa022e092c - path: output/cellranger/sample-123/outs/filtered_feature_bc_matrix.h5 From a0747b1405d817261a3738fc4c11c3dd61103257 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Fri, 10 Jun 2022 11:53:28 +0200 Subject: [PATCH 11/11] Remove empty file md5sum --- tests/modules/cellranger/mkfastq/test.yml | 2 -- 1 file changed, 2 deletions(-) diff --git a/tests/modules/cellranger/mkfastq/test.yml b/tests/modules/cellranger/mkfastq/test.yml index 890f2557..273d8fca 100644 --- a/tests/modules/cellranger/mkfastq/test.yml +++ b/tests/modules/cellranger/mkfastq/test.yml @@ -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