diff --git a/modules.json b/modules.json index 2d534b26..13cc228c 100644 --- a/modules.json +++ b/modules.json @@ -17,27 +17,27 @@ }, "cellranger/count": { "branch": "master", - "git_sha": "c93c5a87d7ea1aef0b81a64d6e6b00bdb79d52c2", + "git_sha": "a772a68aab0866ed10a020443beaedd987d8d690", "installed_by": ["modules"] }, "cellranger/mkgtf": { "branch": "master", - "git_sha": "c93c5a87d7ea1aef0b81a64d6e6b00bdb79d52c2", + "git_sha": "a772a68aab0866ed10a020443beaedd987d8d690", "installed_by": ["modules"] }, "cellranger/mkref": { "branch": "master", - "git_sha": "c93c5a87d7ea1aef0b81a64d6e6b00bdb79d52c2", + "git_sha": "a772a68aab0866ed10a020443beaedd987d8d690", "installed_by": ["modules"] }, "cellranger/mkvdjref": { "branch": "master", - "git_sha": "c93c5a87d7ea1aef0b81a64d6e6b00bdb79d52c2", + "git_sha": "a772a68aab0866ed10a020443beaedd987d8d690", "installed_by": ["modules"] }, "cellranger/multi": { "branch": "master", - "git_sha": "80db11d5d10e7319937c674afabc563bb14e3d93", + "git_sha": "a772a68aab0866ed10a020443beaedd987d8d690", "installed_by": ["modules"] }, "cellrangerarc/count": { diff --git a/modules/nf-core/cellranger/count/main.nf b/modules/nf-core/cellranger/count/main.nf index 51d82397..6f9bedf7 100644 --- a/modules/nf-core/cellranger/count/main.nf +++ b/modules/nf-core/cellranger/count/main.nf @@ -2,7 +2,7 @@ process CELLRANGER_COUNT { tag "$meta.id" label 'process_high' - container "nf-core/cellranger:9.0.1" + container "nf-core/cellranger:10.0.0" input: tuple val(meta), path(reads, stageAs: "fastq_???/*") diff --git a/modules/nf-core/cellranger/count/meta.yml b/modules/nf-core/cellranger/count/meta.yml index 046faf9f..7a1c9f2f 100644 --- a/modules/nf-core/cellranger/count/meta.yml +++ b/modules/nf-core/cellranger/count/meta.yml @@ -36,26 +36,28 @@ input: throws an error if a pair of R1 and R2 fastq files does not have the same filename except for the "_R1"/"_R2" part. Renaming the files does not affect the results (see README.md for detailed tests). pattern: "*{R1,R2}*.fastq.gz" - - - reference: - type: directory - description: Folder containing all the reference indices needed by Cell Ranger + ontologies: [] + - reference: + type: directory + description: Folder containing all the reference indices needed by Cell Ranger output: - - outs: - - meta: - type: file - description: Files containing the outputs of Cell Ranger, see official 10X Genomics - documentation for a complete list - pattern: "${meta.id}/outs/*" + outs: + - - meta: + type: map + description: Groovy Map containing sample information - "**/outs/**": type: file - description: Files containing the outputs of Cell Ranger, see official 10X Genomics - documentation for a complete list + description: Files containing the outputs of Cell Ranger, see official 10X + Genomics documentation for a complete list pattern: "${meta.id}/outs/*" - - versions: - - versions.yml: - type: file - description: File containing software version - pattern: "versions.yml" + ontologies: [] + versions: + - versions.yml: + type: file + description: File containing software version + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML authors: - "@ggabernet" - "@edmundmiller" diff --git a/modules/nf-core/cellranger/count/tests/main.nf.test b/modules/nf-core/cellranger/count/tests/main.nf.test index 3029c0ca..dacdc88e 100644 --- a/modules/nf-core/cellranger/count/tests/main.nf.test +++ b/modules/nf-core/cellranger/count/tests/main.nf.test @@ -60,15 +60,19 @@ nextflow_process { process.out.versions, process.out.outs[0][1].findAll { file(it).name !in [ 'web_summary.html', // unstable checksum + 'possorted_genome_bam.bam.bai', // unstable checksum despite identical content, verified with samtools idxstats + 'possorted_genome_bam.bam', // unstable checksum due to header 'barcodes.tsv.gz' // empty file in test data -> would raise linting error - ]} + ]} + [ + "possorted_genome_bam_samlines:" + sam(process.out.outs.get(0).get(1).find { file(it).name == "possorted_genome_bam.bam" }).getSamLinesMD5() // checksum is unstable when header is included + ], ).match() }, { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'web_summary.html' }).exists() }, - { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'barcodes.tsv.gz' }).exists() } + { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'barcodes.tsv.gz' }).exists() }, + { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'possorted_genome_bam.bam.bai' }).exists() }, ) } - } test("10x example file - stub") { diff --git a/modules/nf-core/cellranger/count/tests/main.nf.test.snap b/modules/nf-core/cellranger/count/tests/main.nf.test.snap index f54fb831..907fcbb5 100644 --- a/modules/nf-core/cellranger/count/tests/main.nf.test.snap +++ b/modules/nf-core/cellranger/count/tests/main.nf.test.snap @@ -2,26 +2,25 @@ "10x example file": { "content": [ [ - "versions.yml:md5,0dc3a237aed20a1af22efdadc21222f8" + "versions.yml:md5,0d99b1cd733a51d67540d796e6b1e1f6" ], [ - "filtered_feature_bc_matrix.h5:md5,da1c5757a060b18d37c7009440f2a3ec", + "filtered_feature_bc_matrix.h5:md5,530804f5b2fdc9d262b4b6d32bde8b7b", "features.tsv.gz:md5,9f93621be0bede2b75596ad255607633", - "matrix.mtx.gz:md5,62dbded3ef45337a019cce26b0a05c98", - "metrics_summary.csv:md5,ca698c488b1d9e7942d31645f7f6c080", - "molecule_info.h5:md5,dafc840adf71e1b36e35b5e34dba77b1", - "possorted_genome_bam.bam:md5,dc049209801a56ded49cc2dfde19ede3", - "possorted_genome_bam.bam.bai:md5,9e82f162fe4729c1d9f48d20c8689648", - "raw_feature_bc_matrix.h5:md5,32920fde374505367b0cfeafb7368cf7", + "matrix.mtx.gz:md5,925a0f46932cba157c44cb94e0c06314", + "metrics_summary.csv:md5,14a544ef1204f4f9d128bc15febb94cf", + "molecule_info.h5:md5,ac30e998aae699f09978be60d548635c", + "raw_feature_bc_matrix.h5:md5,803d3ffa688dccd898c073b300c23ff9", "features.tsv.gz:md5,9f93621be0bede2b75596ad255607633", - "matrix.mtx.gz:md5,b7fa476c92b8ad8f04c10e0119b218b4" + "matrix.mtx.gz:md5,a030e644e8b57df71142e9e26c306b5e", + "possorted_genome_bam_samlines:14b70a2253bcaf40b1c6428e5b66f7a0" ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nf-test": "0.9.3", + "nextflow": "25.04.0" }, - "timestamp": "2025-04-24T14:13:52.226355059" + "timestamp": "2025-11-17T20:10:26.403736028" }, "10x example file - stub": { "content": [ @@ -37,7 +36,7 @@ ] ], "1": [ - "versions.yml:md5,c7ef25b3465ec73fe7704df709b2bcb1" + "versions.yml:md5,292b87e293f0fc9ee9456bf43a359dbd" ], "outs": [ [ @@ -50,14 +49,14 @@ ] ], "versions": [ - "versions.yml:md5,c7ef25b3465ec73fe7704df709b2bcb1" + "versions.yml:md5,292b87e293f0fc9ee9456bf43a359dbd" ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nf-test": "0.9.3", + "nextflow": "25.04.0" }, - "timestamp": "2025-04-24T14:15:54.371712887" + "timestamp": "2025-11-17T15:58:11.185264005" } } \ No newline at end of file diff --git a/modules/nf-core/cellranger/mkgtf/main.nf b/modules/nf-core/cellranger/mkgtf/main.nf index 4d8f7e09..9669e649 100644 --- a/modules/nf-core/cellranger/mkgtf/main.nf +++ b/modules/nf-core/cellranger/mkgtf/main.nf @@ -2,7 +2,7 @@ process CELLRANGER_MKGTF { tag "$gtf" label 'process_low' - container "nf-core/cellranger:9.0.1" + container "nf-core/cellranger:10.0.0" input: path gtf diff --git a/modules/nf-core/cellranger/mkgtf/meta.yml b/modules/nf-core/cellranger/mkgtf/meta.yml index ceaca540..0c0fe6fd 100644 --- a/modules/nf-core/cellranger/mkgtf/meta.yml +++ b/modules/nf-core/cellranger/mkgtf/meta.yml @@ -16,21 +16,24 @@ tools: licence: [10X Genomics EULA] identifier: "" input: - - - gtf: - type: file - description: The reference GTF transcriptome file - pattern: "*.gtf" -output: - gtf: - - "*.gtf": - type: directory - description: The filtered GTF transcriptome file - pattern: "*.filtered.gtf" - - versions: - - versions.yml: - type: file - description: File containing software version - pattern: "versions.yml" + type: file + description: The reference GTF transcriptome file + pattern: "*.gtf" + ontologies: [] +output: + gtf: + - "*.gtf": + type: directory + description: The filtered GTF transcriptome file + pattern: "*.filtered.gtf" + versions: + - versions.yml: + type: file + description: File containing software version + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML authors: - "@ggabernet" - "@edmundmiller" diff --git a/modules/nf-core/cellranger/mkgtf/tests/main.nf.test.snap b/modules/nf-core/cellranger/mkgtf/tests/main.nf.test.snap index 5877de4a..560c5a91 100644 --- a/modules/nf-core/cellranger/mkgtf/tests/main.nf.test.snap +++ b/modules/nf-core/cellranger/mkgtf/tests/main.nf.test.snap @@ -6,21 +6,21 @@ "genome.filtered.gtf:md5,50fc877b1c53b36b3b413aff88bda48c" ], "1": [ - "versions.yml:md5,708c6b98134cdeaa8a48b764ba952628" + "versions.yml:md5,3cef4e22f792ddce926816fb266c5157" ], "gtf": [ "genome.filtered.gtf:md5,50fc877b1c53b36b3b413aff88bda48c" ], "versions": [ - "versions.yml:md5,708c6b98134cdeaa8a48b764ba952628" + "versions.yml:md5,3cef4e22f792ddce926816fb266c5157" ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nf-test": "0.9.3", + "nextflow": "25.04.0" }, - "timestamp": "2025-04-24T14:46:28.244866661" + "timestamp": "2025-11-17T16:00:19.670697898" }, "homo_sapiens - reference - stub": { "content": [ @@ -29,20 +29,20 @@ "genome.filtered.gtf:md5,d41d8cd98f00b204e9800998ecf8427e" ], "1": [ - "versions.yml:md5,708c6b98134cdeaa8a48b764ba952628" + "versions.yml:md5,3cef4e22f792ddce926816fb266c5157" ], "gtf": [ "genome.filtered.gtf:md5,d41d8cd98f00b204e9800998ecf8427e" ], "versions": [ - "versions.yml:md5,708c6b98134cdeaa8a48b764ba952628" + "versions.yml:md5,3cef4e22f792ddce926816fb266c5157" ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nf-test": "0.9.3", + "nextflow": "25.04.0" }, - "timestamp": "2025-04-24T14:47:15.161383742" + "timestamp": "2025-11-17T16:00:24.880586344" } } \ No newline at end of file diff --git a/modules/nf-core/cellranger/mkref/main.nf b/modules/nf-core/cellranger/mkref/main.nf index b0218939..d3c56db2 100644 --- a/modules/nf-core/cellranger/mkref/main.nf +++ b/modules/nf-core/cellranger/mkref/main.nf @@ -2,7 +2,7 @@ process CELLRANGER_MKREF { tag "$fasta" label 'process_high' - container "nf-core/cellranger:9.0.1" + container "nf-core/cellranger:10.0.0" input: path fasta diff --git a/modules/nf-core/cellranger/mkref/meta.yml b/modules/nf-core/cellranger/mkref/meta.yml index f4f59563..4ffaf6fe 100644 --- a/modules/nf-core/cellranger/mkref/meta.yml +++ b/modules/nf-core/cellranger/mkref/meta.yml @@ -16,28 +16,32 @@ tools: licence: [10X Genomics EULA] identifier: "" input: - - - fasta: - type: file - description: Reference genome FASTA file - pattern: "*.{fasta,fa}" - - - gtf: - type: file - description: Reference transcriptome GTF file - pattern: "*.gtf" - - - reference_name: - type: string - description: The name to give the new reference folder - pattern: str + - fasta: + type: file + description: Reference genome FASTA file + pattern: "*.{fasta,fa}" + ontologies: [] + - gtf: + type: file + description: Reference transcriptome GTF file + pattern: "*.gtf" + ontologies: [] + - reference_name: + type: string + description: The name to give the new reference folder + pattern: str output: - - reference: - - ${reference_name}: - type: directory - description: Folder containing all the reference indices needed by Cell Ranger - - versions: - - versions.yml: - type: file - description: File containing software version - pattern: "versions.yml" + reference: + - ${reference_name}: + type: directory + description: Folder containing all the reference indices needed by Cell Ranger + versions: + - versions.yml: + type: file + description: File containing software version + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML authors: - "@ggabernet" maintainers: diff --git a/modules/nf-core/cellranger/mkref/tests/main.nf.test.snap b/modules/nf-core/cellranger/mkref/tests/main.nf.test.snap index 45e49a93..b4266232 100644 --- a/modules/nf-core/cellranger/mkref/tests/main.nf.test.snap +++ b/modules/nf-core/cellranger/mkref/tests/main.nf.test.snap @@ -8,7 +8,7 @@ [ "genes.gtf.gz:md5,50fc877b1c53b36b3b413aff88bda48c" ], - "reference.json:md5,36a50e2bcb2aa0c15d102e30be5fc488", + "reference.json:md5,5a9c9db6804ec625d50a16ccc079a1eb", "SA:md5,bcf3e1a855783105150b46c905465333", "SAindex:md5,b93fb07d342e6c32a00ebc4311c0ad38", "Genome:md5,22102926fadf5890e905ca71b2da3f35", @@ -17,14 +17,14 @@ "exonInfo.tab:md5,0d560290fab688b7268d88d5494bf9fe", "sjdbList.out.tab:md5,9e4f991abbbfeb3935a2bb21b9e258f1", [ - "versions.yml:md5,8f36be9d97f8563921791dbeb0ea9a75" + "versions.yml:md5,c8c9dfcd3af617a7c147a75ded89ccd9" ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nf-test": "0.9.3", + "nextflow": "25.04.0" }, - "timestamp": "2025-04-25T10:06:03.277296893" + "timestamp": "2025-11-17T16:00:38.566253697" }, "homo_sapiens - reference - stub": { "content": [ @@ -35,7 +35,7 @@ ] ], "1": [ - "versions.yml:md5,8f36be9d97f8563921791dbeb0ea9a75" + "versions.yml:md5,c8c9dfcd3af617a7c147a75ded89ccd9" ], "reference": [ [ @@ -43,14 +43,14 @@ ] ], "versions": [ - "versions.yml:md5,8f36be9d97f8563921791dbeb0ea9a75" + "versions.yml:md5,c8c9dfcd3af617a7c147a75ded89ccd9" ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nf-test": "0.9.3", + "nextflow": "25.04.0" }, - "timestamp": "2025-04-25T10:06:20.297698461" + "timestamp": "2025-11-17T16:00:43.531859482" } } \ No newline at end of file diff --git a/modules/nf-core/cellranger/mkvdjref/main.nf b/modules/nf-core/cellranger/mkvdjref/main.nf index 0c4a3f35..5f27a347 100644 --- a/modules/nf-core/cellranger/mkvdjref/main.nf +++ b/modules/nf-core/cellranger/mkvdjref/main.nf @@ -2,7 +2,7 @@ process CELLRANGER_MKVDJREF { tag "$fasta" label 'process_high' - container "nf-core/cellranger:9.0.1" + container "nf-core/cellranger:10.0.0" input: path fasta // optional diff --git a/modules/nf-core/cellranger/mkvdjref/meta.yml b/modules/nf-core/cellranger/mkvdjref/meta.yml index 23605d3f..2adb129f 100644 --- a/modules/nf-core/cellranger/mkvdjref/meta.yml +++ b/modules/nf-core/cellranger/mkvdjref/meta.yml @@ -22,34 +22,39 @@ tools: licence: ["10x Genomics EULA"] identifier: "" input: - - - fasta: - type: file - description: Reference genome FASTA file (optional) - pattern: "*.{fasta,fa}" - - - gtf: - type: file - description: Reference genome GTF file (optional) - pattern: "*.gtf" - - - seqs: - type: file - description: Reference genome FASTA file from the 10X Genomics fetch-imgt workflow - (optional) - pattern: "*.{fasta,fa}" - - - reference_name: - type: string - description: The name to give the new reference folder, e.g. `my_vdj_ref`. This - flag is required - pattern: str + - fasta: + type: file + description: Reference genome FASTA file (optional) + pattern: "*.{fasta,fa}" + ontologies: [] + - gtf: + type: file + description: Reference genome GTF file (optional) + pattern: "*.gtf" + ontologies: [] + - seqs: + type: file + description: Reference genome FASTA file from the 10X Genomics fetch-imgt workflow + (optional) + pattern: "*.{fasta,fa}" + ontologies: [] + - reference_name: + type: string + description: The name to give the new reference folder, e.g. `my_vdj_ref`. This + flag is required + pattern: str output: - - reference: - - ${reference_name}: - type: directory - description: Folder containing all the reference indices needed by Cell Ranger - - versions: - - versions.yml: - type: file - description: File containing software version - pattern: "versions.yml" + reference: + - ${reference_name}: + type: directory + description: Folder containing all the reference indices needed by Cell Ranger + versions: + - versions.yml: + type: file + description: File containing software version + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML authors: - "@ggabernet" - "@klkeys" diff --git a/modules/nf-core/cellranger/mkvdjref/tests/main.nf.test.snap b/modules/nf-core/cellranger/mkvdjref/tests/main.nf.test.snap index a2529f6d..b2f12b42 100644 --- a/modules/nf-core/cellranger/mkvdjref/tests/main.nf.test.snap +++ b/modules/nf-core/cellranger/mkvdjref/tests/main.nf.test.snap @@ -7,30 +7,30 @@ [ "regions.fa:md5,1e22fd84ab26c89d3c285140df2daf5f" ], - "reference.json:md5,64fab77b52134ee22033d9540bd66639" + "reference.json:md5,b128ff77eac9ad9b11b399dbb3b3c019" ] ], "1": [ - "versions.yml:md5,55e958337b93e96c5257ab894ee59091" + "versions.yml:md5,4769691097415606679895ffb694ca95" ], "reference": [ [ [ "regions.fa:md5,1e22fd84ab26c89d3c285140df2daf5f" ], - "reference.json:md5,64fab77b52134ee22033d9540bd66639" + "reference.json:md5,b128ff77eac9ad9b11b399dbb3b3c019" ] ], "versions": [ - "versions.yml:md5,55e958337b93e96c5257ab894ee59091" + "versions.yml:md5,4769691097415606679895ffb694ca95" ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nf-test": "0.9.3", + "nextflow": "25.04.0" }, - "timestamp": "2025-04-25T11:05:52.416630198" + "timestamp": "2025-11-17T16:02:21.968411746" }, "homo_sapiens - vdj - reference - stub": { "content": [ @@ -44,7 +44,7 @@ ] ], "1": [ - "versions.yml:md5,55e958337b93e96c5257ab894ee59091" + "versions.yml:md5,4769691097415606679895ffb694ca95" ], "reference": [ [ @@ -55,14 +55,14 @@ ] ], "versions": [ - "versions.yml:md5,55e958337b93e96c5257ab894ee59091" + "versions.yml:md5,4769691097415606679895ffb694ca95" ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nf-test": "0.9.3", + "nextflow": "25.04.0" }, - "timestamp": "2025-04-25T11:06:08.980256548" + "timestamp": "2025-11-17T16:02:26.890408192" } } \ No newline at end of file diff --git a/modules/nf-core/cellranger/multi/main.nf b/modules/nf-core/cellranger/multi/main.nf index f4bc4cde..54a1be1b 100644 --- a/modules/nf-core/cellranger/multi/main.nf +++ b/modules/nf-core/cellranger/multi/main.nf @@ -2,7 +2,7 @@ process CELLRANGER_MULTI { tag "$meta.id" label 'process_high' - container "nf-core/cellranger:9.0.1" + container "nf-core/cellranger:10.0.0" input: val meta diff --git a/modules/nf-core/cellranger/multi/tests/main.nf.test.snap b/modules/nf-core/cellranger/multi/tests/main.nf.test.snap index 8ea980dd..54521dee 100644 --- a/modules/nf-core/cellranger/multi/tests/main.nf.test.snap +++ b/modules/nf-core/cellranger/multi/tests/main.nf.test.snap @@ -17,28 +17,28 @@ "regions.fa:md5,1953406d913fb0fd753c6b56e847da83" ], [ - "all_contig_annotations.json:md5,16ad7120f003d05883a29214377efa6b", "cell_barcodes.json:md5,d751713988987e9331980363e24189ce", + "all_contig_annotations.json:md5,cf33174fc4dbbadc5e74051bc13a5bd2", "reference.json:md5,384f6efabad59f6da5c89b862aee71a8" ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nf-test": "0.9.3", + "nextflow": "25.04.0" }, - "timestamp": "2025-04-28T10:09:47.792282434" + "timestamp": "2025-11-17T16:05:50.574012495" }, "versions-PBMC": { "content": [ [ - "versions.yml:md5,3d75b44017b2d623dfb9aa8b89538b4d" + "versions.yml:md5,1e16f7d40ef563f7d0a24f8944374d4d" ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nf-test": "0.9.3", + "nextflow": "25.04.0" }, - "timestamp": "2025-04-28T10:09:47.86424328" + "timestamp": "2025-11-17T16:05:50.585897865" }, "cellranger - multi - 10k - PBMC - with cmo": { "content": [ @@ -58,76 +58,76 @@ "regions.fa:md5,1953406d913fb0fd753c6b56e847da83" ], [ - "all_contig_annotations.json:md5,474e6ca846176111c8003ec7cedc299e", "cell_barcodes.json:md5,d751713988987e9331980363e24189ce", + "all_contig_annotations.json:md5,7cc7d06c7650d20c7330513ae2e383bf", "reference.json:md5,384f6efabad59f6da5c89b862aee71a8" ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nf-test": "0.9.3", + "nextflow": "25.04.0" }, - "timestamp": "2025-04-28T10:18:16.990217751" + "timestamp": "2025-11-17T16:09:13.334801399" }, "versions-with-cmo": { "content": [ [ - "versions.yml:md5,3d75b44017b2d623dfb9aa8b89538b4d" + "versions.yml:md5,1e16f7d40ef563f7d0a24f8944374d4d" ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nf-test": "0.9.3", + "nextflow": "25.04.0" }, - "timestamp": "2025-04-28T10:18:17.058412204" + "timestamp": "2025-11-17T16:09:13.35185767" }, "cellranger - multi - 5k - a549 - sc3 v3 - gex + crispr": { "content": [ [ - "metrics_summary.csv:md5,9c9749b6b5c5e17acb23405f1a33a53b" + "metrics_summary.csv:md5,a51dcadefdd5b76cee5c3d4340181a5a" ], [ - "raw_feature_bc_matrix.h5:md5,fc98a3d47af1091763e94ed4a79f8f15" + "raw_feature_bc_matrix.h5:md5,01c558f6a5b96cd40b1ed41217164460" ], [ - "sample_filtered_feature_bc_matrix.h5:md5,63cb76a43b82c4e0083c4db9e8f5c980" + "sample_filtered_feature_bc_matrix.h5:md5,8903d36c96c4de869eba434c4722817d" ], [ - "protospacer_calls_per_cell.csv:md5,a94184bddcd8107421f62986b9e0984a" + ], [ - "perturbation_efficiencies_by_feature.csv:md5,bdf16f59c33b5f061e87b4f3ed74e809" + ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nf-test": "0.9.3", + "nextflow": "25.04.0" }, - "timestamp": "2025-04-28T10:28:49.150344674" + "timestamp": "2025-11-17T16:15:30.316175106" }, "versions-a549-crispr": { "content": [ [ - "versions.yml:md5,3d75b44017b2d623dfb9aa8b89538b4d" + "versions.yml:md5,1e16f7d40ef563f7d0a24f8944374d4d" ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nf-test": "0.9.3", + "nextflow": "25.04.0" }, - "timestamp": "2025-04-28T10:28:49.23707814" + "timestamp": "2025-11-17T16:15:30.339721973" }, "versions-with-vdj": { "content": [ [ - "versions.yml:md5,3d75b44017b2d623dfb9aa8b89538b4d" + "versions.yml:md5,1e16f7d40ef563f7d0a24f8944374d4d" ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nf-test": "0.9.3", + "nextflow": "25.04.0" }, - "timestamp": "2025-04-28T10:23:10.585307273" + "timestamp": "2025-11-17T16:12:35.380645061" }, "cellranger - multi - 10k - PBMC - with vdj": { "content": [ @@ -147,15 +147,15 @@ "regions.fa:md5,1953406d913fb0fd753c6b56e847da83" ], [ - "all_contig_annotations.json:md5,e4e09b4368470f55da786e424ae2fdd8", "cell_barcodes.json:md5,d751713988987e9331980363e24189ce", + "all_contig_annotations.json:md5,dadfaf5ce1daff9f2454d012837bd58b", "reference.json:md5,384f6efabad59f6da5c89b862aee71a8" ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nf-test": "0.9.3", + "nextflow": "25.04.0" }, - "timestamp": "2025-04-28T10:23:10.520491466" + "timestamp": "2025-11-17T16:12:35.359552127" } } \ No newline at end of file diff --git a/subworkflows/local/align_cellrangermulti.nf b/subworkflows/local/align_cellrangermulti.nf index 3b12b02b..581df76d 100644 --- a/subworkflows/local/align_cellrangermulti.nf +++ b/subworkflows/local/align_cellrangermulti.nf @@ -234,10 +234,14 @@ def parse_demultiplexed_output_channels(in_ch, pattern) { meta_clone.input_type = pattern.contains('raw_') ? 'raw' : 'filtered' // add metadata for conversion workflow if ( mtx_files.toString().contains("per_sample_outs") ) { def demultiplexed_sample_id = mtx_files.toString().split('/per_sample_outs/')[1].split('/')[0] + if ( demultiplexed_sample_id.toString() == meta.id) { + return null + } meta_clone.id = demultiplexed_sample_id.toString() } [ meta_clone, mtx_files ] } // check if output is from demultiplexed sample, if yes, correct meta.id for proper conversion naming + .filter{ it != null } // remove nulls from previous step .groupTuple( by: 0 ) // group it back as one file collection per sample return out_ch diff --git a/tests/main_pipeline_cellranger.nf.test.snap b/tests/main_pipeline_cellranger.nf.test.snap index a8d98e06..caa75a15 100644 --- a/tests/main_pipeline_cellranger.nf.test.snap +++ b/tests/main_pipeline_cellranger.nf.test.snap @@ -4,13 +4,13 @@ 20, { "CELLRANGER_COUNT": { - "cellranger": "9.0.1 " + "cellranger": "cellranger 10.0.0 " }, "CELLRANGER_MKGTF": { - "cellranger": "9.0.1" + "cellranger": "10.0.0" }, "CELLRANGER_MKREF": { - "cellranger": "9.0.1" + "cellranger": "10.0.0" }, "FASTQC": { "fastqc": "0.12.1" @@ -319,16 +319,16 @@ [ "barcodes.tsv.gz:md5,fe6e51564b4405b37ca8604a844b1f2e", "features.tsv.gz:md5,99e453cb1443a3e43e99405184e51a5e", - "matrix.mtx.gz:md5,76991485c25e90a3553993d6a55df6bd", + "matrix.mtx.gz:md5,53541adad167e7af8a1c2dcf36b5da00", "barcodes.tsv.gz:md5,85da6b6e0c78dfe81af8c07c2017ab5e", "features.tsv.gz:md5,99e453cb1443a3e43e99405184e51a5e", - "matrix.mtx.gz:md5,195ae8a9089e16ad19d8c9d05277f99f", + "matrix.mtx.gz:md5,398383fe8a29cdccdf23f036116d7a6c", "barcodes.tsv.gz:md5,77afe9a76631fc7b44236d3962a55aa5", "features.tsv.gz:md5,99e453cb1443a3e43e99405184e51a5e", - "matrix.mtx.gz:md5,5fc86fb6808aa997ee791b5dae2214de", + "matrix.mtx.gz:md5,99faf91259889de6bd6dbafe9ae1cd25", "barcodes.tsv.gz:md5,081f72b5252ccaf5ffd535ffbd235c4c", "features.tsv.gz:md5,99e453cb1443a3e43e99405184e51a5e", - "matrix.mtx.gz:md5,563a2e93bc9b7c6825e543f71da785d2", + "matrix.mtx.gz:md5,0d57e727d649efcd3fc6b4cd0067bfe0", "GRCm38.p6.genome.chr19_genes.filtered.gtf:md5,956caa7c851df640ded6c3f5f1a7cd41", "genome.fa:md5,ef1ae316990b7c77fd0baa0a89b75a6d", "genome.fa.fai:md5,729bb811dc9ababd5ee35029b8140f36", @@ -359,7 +359,7 @@ "Sample_Y_raw_matrix.h5ad:md5,d5c3a30bcd4d8011eb5aa39ad0f1c286", "Sample_Y_raw_matrix.sce.rds:md5,061ab8ba3ed28e6312c0367a2a9dfeb3", "Sample_Y_raw_matrix.seurat.rds:md5,3f4a3e6529b10c646fd08173d5baa339", - "cellranger-count-stats-table.txt:md5,dcfc25c2bb422c5f279af728c8b62f58", + "cellranger-count-stats-table.txt:md5,b596a1ed25c8dba1ff3026db56dc5f5d", "cellranger-count-warnings-table.txt:md5,f257d0a84efc395072a517db643b7935", "fastqc-status-check-heatmap.txt:md5,d122badcaa647409c35a809e8a127f99", "fastqc_adapter_content_plot.txt:md5,25f2bf3896afee60c3af1c2d406adb2a", @@ -373,16 +373,16 @@ "mqc_cellranger_count_bc_knee.txt:md5,a4482a60b1d048a2d830505c766c8395", "mqc_cellranger_count_genesXcell.txt:md5,a691c27c313cb32203b42d678686243b", "mqc_cellranger_count_saturation.txt:md5,4ce68b5a0b43a212ca07d9592c4174c5", - "multiqc_cellranger_count.txt:md5,da890b424a8a53f40acc12a2766e627f", + "multiqc_cellranger_count.txt:md5,997745b8a1015fc74ffbe8ec35056f8d", "multiqc_citations.txt:md5,db9f58c039af2923e06a61e46e82c015", "multiqc_fastqc.txt:md5,12027880857508ce5cedc3904a351730", "multiqc_general_stats.txt:md5,92a7a66e313e6ce2d13da53b501b5c0c" ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-10-23T19:11:11.981129882" + "timestamp": "2025-11-20T17:40:14.32703797" } } \ No newline at end of file diff --git a/tests/main_pipeline_cellrangermulti.nf.test.snap b/tests/main_pipeline_cellrangermulti.nf.test.snap index c0552368..aadcbc67 100644 --- a/tests/main_pipeline_cellrangermulti.nf.test.snap +++ b/tests/main_pipeline_cellrangermulti.nf.test.snap @@ -1,19 +1,19 @@ { "test-dataset_cellrangermulti_aligner_human": { "content": [ - 57, + 65, { "CELLRANGER_MKGTF": { - "cellranger": "9.0.1" + "cellranger": "10.0.0" }, "CELLRANGER_MKREF": { - "cellranger": "9.0.1" + "cellranger": "10.0.0" }, "CELLRANGER_MKVDJREF": { - "cellranger": "9.0.1" + "cellranger": "10.0.0" }, "CELLRANGER_MULTI": { - "cellranger": "9.0.1 " + "cellranger": "cellranger 10.0.0 " }, "FASTQC": { "fastqc": "0.12.1" @@ -37,475 +37,462 @@ "cellrangermulti/count/4PLEX_HUMAN", "cellrangermulti/count/4PLEX_HUMAN/outs", "cellrangermulti/count/4PLEX_HUMAN/outs/config.csv", - "cellrangermulti/count/4PLEX_HUMAN/outs/multi", - "cellrangermulti/count/4PLEX_HUMAN/outs/multi/count", - "cellrangermulti/count/4PLEX_HUMAN/outs/multi/count/raw_cloupe.cloupe", - "cellrangermulti/count/4PLEX_HUMAN/outs/multi/count/raw_feature_bc_matrix", - "cellrangermulti/count/4PLEX_HUMAN/outs/multi/count/raw_feature_bc_matrix.h5", - "cellrangermulti/count/4PLEX_HUMAN/outs/multi/count/raw_feature_bc_matrix/barcodes.tsv.gz", - "cellrangermulti/count/4PLEX_HUMAN/outs/multi/count/raw_feature_bc_matrix/features.tsv.gz", - "cellrangermulti/count/4PLEX_HUMAN/outs/multi/count/raw_feature_bc_matrix/matrix.mtx.gz", - "cellrangermulti/count/4PLEX_HUMAN/outs/multi/count/raw_molecule_info.h5", - "cellrangermulti/count/4PLEX_HUMAN/outs/multi/count/raw_probe_bc_matrix.h5", - "cellrangermulti/count/4PLEX_HUMAN/outs/multi/count/unassigned_alignments.bam", - "cellrangermulti/count/4PLEX_HUMAN/outs/multi/count/unassigned_alignments.bam.bai", - "cellrangermulti/count/4PLEX_HUMAN/outs/multi/multiplexing_analysis", - "cellrangermulti/count/4PLEX_HUMAN/outs/multi/multiplexing_analysis/cells_per_tag.json", - "cellrangermulti/count/4PLEX_HUMAN/outs/multi/multiplexing_analysis/frp_gem_barcode_overlap.csv", + "cellrangermulti/count/4PLEX_HUMAN/outs/filtered_feature_bc_matrix", + "cellrangermulti/count/4PLEX_HUMAN/outs/filtered_feature_bc_matrix.h5", + "cellrangermulti/count/4PLEX_HUMAN/outs/filtered_feature_bc_matrix/barcodes.tsv.gz", + "cellrangermulti/count/4PLEX_HUMAN/outs/filtered_feature_bc_matrix/features.tsv.gz", + "cellrangermulti/count/4PLEX_HUMAN/outs/filtered_feature_bc_matrix/matrix.mtx.gz", + "cellrangermulti/count/4PLEX_HUMAN/outs/multiplexing_analysis", + "cellrangermulti/count/4PLEX_HUMAN/outs/multiplexing_analysis/cells_per_tag.json", + "cellrangermulti/count/4PLEX_HUMAN/outs/multiplexing_analysis/frp_gem_barcode_overlap.csv", "cellrangermulti/count/4PLEX_HUMAN/outs/per_sample_outs", "cellrangermulti/count/4PLEX_HUMAN/outs/per_sample_outs/Colorectal_BC3", - "cellrangermulti/count/4PLEX_HUMAN/outs/per_sample_outs/Colorectal_BC3/count", - "cellrangermulti/count/4PLEX_HUMAN/outs/per_sample_outs/Colorectal_BC3/count/analysis", - "cellrangermulti/count/4PLEX_HUMAN/outs/per_sample_outs/Colorectal_BC3/count/analysis/clustering", - "cellrangermulti/count/4PLEX_HUMAN/outs/per_sample_outs/Colorectal_BC3/count/analysis/clustering/gene_expression_graphclust", - "cellrangermulti/count/4PLEX_HUMAN/outs/per_sample_outs/Colorectal_BC3/count/analysis/clustering/gene_expression_graphclust/clusters.csv", - "cellrangermulti/count/4PLEX_HUMAN/outs/per_sample_outs/Colorectal_BC3/count/analysis/clustering/gene_expression_kmeans_10_clusters", - "cellrangermulti/count/4PLEX_HUMAN/outs/per_sample_outs/Colorectal_BC3/count/analysis/clustering/gene_expression_kmeans_10_clusters/clusters.csv", - "cellrangermulti/count/4PLEX_HUMAN/outs/per_sample_outs/Colorectal_BC3/count/analysis/clustering/gene_expression_kmeans_2_clusters", - "cellrangermulti/count/4PLEX_HUMAN/outs/per_sample_outs/Colorectal_BC3/count/analysis/clustering/gene_expression_kmeans_2_clusters/clusters.csv", - "cellrangermulti/count/4PLEX_HUMAN/outs/per_sample_outs/Colorectal_BC3/count/analysis/clustering/gene_expression_kmeans_3_clusters", - "cellrangermulti/count/4PLEX_HUMAN/outs/per_sample_outs/Colorectal_BC3/count/analysis/clustering/gene_expression_kmeans_3_clusters/clusters.csv", - "cellrangermulti/count/4PLEX_HUMAN/outs/per_sample_outs/Colorectal_BC3/count/analysis/clustering/gene_expression_kmeans_4_clusters", - "cellrangermulti/count/4PLEX_HUMAN/outs/per_sample_outs/Colorectal_BC3/count/analysis/clustering/gene_expression_kmeans_4_clusters/clusters.csv", - "cellrangermulti/count/4PLEX_HUMAN/outs/per_sample_outs/Colorectal_BC3/count/analysis/clustering/gene_expression_kmeans_5_clusters", - "cellrangermulti/count/4PLEX_HUMAN/outs/per_sample_outs/Colorectal_BC3/count/analysis/clustering/gene_expression_kmeans_5_clusters/clusters.csv", - "cellrangermulti/count/4PLEX_HUMAN/outs/per_sample_outs/Colorectal_BC3/count/analysis/clustering/gene_expression_kmeans_6_clusters", - "cellrangermulti/count/4PLEX_HUMAN/outs/per_sample_outs/Colorectal_BC3/count/analysis/clustering/gene_expression_kmeans_6_clusters/clusters.csv", - "cellrangermulti/count/4PLEX_HUMAN/outs/per_sample_outs/Colorectal_BC3/count/analysis/clustering/gene_expression_kmeans_7_clusters", - "cellrangermulti/count/4PLEX_HUMAN/outs/per_sample_outs/Colorectal_BC3/count/analysis/clustering/gene_expression_kmeans_7_clusters/clusters.csv", - "cellrangermulti/count/4PLEX_HUMAN/outs/per_sample_outs/Colorectal_BC3/count/analysis/clustering/gene_expression_kmeans_8_clusters", - "cellrangermulti/count/4PLEX_HUMAN/outs/per_sample_outs/Colorectal_BC3/count/analysis/clustering/gene_expression_kmeans_8_clusters/clusters.csv", - "cellrangermulti/count/4PLEX_HUMAN/outs/per_sample_outs/Colorectal_BC3/count/analysis/clustering/gene_expression_kmeans_9_clusters", - "cellrangermulti/count/4PLEX_HUMAN/outs/per_sample_outs/Colorectal_BC3/count/analysis/clustering/gene_expression_kmeans_9_clusters/clusters.csv", - "cellrangermulti/count/4PLEX_HUMAN/outs/per_sample_outs/Colorectal_BC3/count/analysis/diffexp", - "cellrangermulti/count/4PLEX_HUMAN/outs/per_sample_outs/Colorectal_BC3/count/analysis/diffexp/gene_expression_graphclust", - "cellrangermulti/count/4PLEX_HUMAN/outs/per_sample_outs/Colorectal_BC3/count/analysis/diffexp/gene_expression_graphclust/differential_expression.csv", - "cellrangermulti/count/4PLEX_HUMAN/outs/per_sample_outs/Colorectal_BC3/count/analysis/diffexp/gene_expression_kmeans_10_clusters", - "cellrangermulti/count/4PLEX_HUMAN/outs/per_sample_outs/Colorectal_BC3/count/analysis/diffexp/gene_expression_kmeans_10_clusters/differential_expression.csv", - "cellrangermulti/count/4PLEX_HUMAN/outs/per_sample_outs/Colorectal_BC3/count/analysis/diffexp/gene_expression_kmeans_2_clusters", - "cellrangermulti/count/4PLEX_HUMAN/outs/per_sample_outs/Colorectal_BC3/count/analysis/diffexp/gene_expression_kmeans_2_clusters/differential_expression.csv", - "cellrangermulti/count/4PLEX_HUMAN/outs/per_sample_outs/Colorectal_BC3/count/analysis/diffexp/gene_expression_kmeans_3_clusters", - 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"cellrangermulti/count/PBMC_10K_CMV/outs/per_sample_outs/PBMC_10K_CMV/sample_alignments.bam.bai", + "cellrangermulti/count/PBMC_10K_CMV/outs/per_sample_outs/PBMC_10K_CMV/sample_cloupe.cloupe", + "cellrangermulti/count/PBMC_10K_CMV/outs/per_sample_outs/PBMC_10K_CMV/sample_filtered_barcodes.csv", + "cellrangermulti/count/PBMC_10K_CMV/outs/per_sample_outs/PBMC_10K_CMV/sample_filtered_feature_bc_matrix", + "cellrangermulti/count/PBMC_10K_CMV/outs/per_sample_outs/PBMC_10K_CMV/sample_filtered_feature_bc_matrix.h5", + "cellrangermulti/count/PBMC_10K_CMV/outs/per_sample_outs/PBMC_10K_CMV/sample_filtered_feature_bc_matrix/barcodes.tsv.gz", + "cellrangermulti/count/PBMC_10K_CMV/outs/per_sample_outs/PBMC_10K_CMV/sample_filtered_feature_bc_matrix/features.tsv.gz", + "cellrangermulti/count/PBMC_10K_CMV/outs/per_sample_outs/PBMC_10K_CMV/sample_filtered_feature_bc_matrix/matrix.mtx.gz", + "cellrangermulti/count/PBMC_10K_CMV/outs/per_sample_outs/PBMC_10K_CMV/sample_molecule_info.h5", + "cellrangermulti/count/PBMC_10K_CMV/outs/per_sample_outs/PBMC_10K_CMV/sample_raw_feature_bc_matrix", + "cellrangermulti/count/PBMC_10K_CMV/outs/per_sample_outs/PBMC_10K_CMV/sample_raw_feature_bc_matrix.h5", + "cellrangermulti/count/PBMC_10K_CMV/outs/per_sample_outs/PBMC_10K_CMV/sample_raw_feature_bc_matrix/barcodes.tsv.gz", + "cellrangermulti/count/PBMC_10K_CMV/outs/per_sample_outs/PBMC_10K_CMV/sample_raw_feature_bc_matrix/features.tsv.gz", + "cellrangermulti/count/PBMC_10K_CMV/outs/per_sample_outs/PBMC_10K_CMV/sample_raw_feature_bc_matrix/matrix.mtx.gz", "cellrangermulti/count/PBMC_10K_CMV/outs/per_sample_outs/PBMC_10K_CMV/vdj_t", "cellrangermulti/count/PBMC_10K_CMV/outs/per_sample_outs/PBMC_10K_CMV/vdj_t/airr_rearrangement.tsv", "cellrangermulti/count/PBMC_10K_CMV/outs/per_sample_outs/PBMC_10K_CMV/vdj_t/cell_barcodes.json", @@ -875,10 +884,30 @@ "cellrangermulti/count/PBMC_10K_CMV/outs/per_sample_outs/PBMC_10K_CMV/vdj_t/filtered_contig_annotations.csv", "cellrangermulti/count/PBMC_10K_CMV/outs/per_sample_outs/PBMC_10K_CMV/vdj_t/vdj_contig_info.pb", "cellrangermulti/count/PBMC_10K_CMV/outs/per_sample_outs/PBMC_10K_CMV/web_summary.html", + "cellrangermulti/count/PBMC_10K_CMV/outs/qc_library_metrics.csv", + "cellrangermulti/count/PBMC_10K_CMV/outs/qc_report.html", + "cellrangermulti/count/PBMC_10K_CMV/outs/qc_sample_metrics.csv", + "cellrangermulti/count/PBMC_10K_CMV/outs/raw_cloupe.cloupe", + "cellrangermulti/count/PBMC_10K_CMV/outs/raw_feature_bc_matrix", + "cellrangermulti/count/PBMC_10K_CMV/outs/raw_feature_bc_matrix.h5", + "cellrangermulti/count/PBMC_10K_CMV/outs/raw_feature_bc_matrix/barcodes.tsv.gz", + "cellrangermulti/count/PBMC_10K_CMV/outs/raw_feature_bc_matrix/features.tsv.gz", + "cellrangermulti/count/PBMC_10K_CMV/outs/raw_feature_bc_matrix/matrix.mtx.gz", + "cellrangermulti/count/PBMC_10K_CMV/outs/raw_molecule_info.h5", + "cellrangermulti/count/PBMC_10K_CMV/outs/unassigned_alignments.bam", + "cellrangermulti/count/PBMC_10K_CMV/outs/unassigned_alignments.bam.bai", "cellrangermulti/count/PBMC_10K_CMV/outs/vdj_reference", "cellrangermulti/count/PBMC_10K_CMV/outs/vdj_reference/fasta", "cellrangermulti/count/PBMC_10K_CMV/outs/vdj_reference/fasta/regions.fa", "cellrangermulti/count/PBMC_10K_CMV/outs/vdj_reference/reference.json", + "cellrangermulti/count/PBMC_10K_CMV/outs/vdj_t", + "cellrangermulti/count/PBMC_10K_CMV/outs/vdj_t/all_contig.bam", + "cellrangermulti/count/PBMC_10K_CMV/outs/vdj_t/all_contig.bam.bai", + "cellrangermulti/count/PBMC_10K_CMV/outs/vdj_t/all_contig.fasta", + "cellrangermulti/count/PBMC_10K_CMV/outs/vdj_t/all_contig.fastq", + "cellrangermulti/count/PBMC_10K_CMV/outs/vdj_t/all_contig_annotations.bed", + "cellrangermulti/count/PBMC_10K_CMV/outs/vdj_t/all_contig_annotations.csv", + "cellrangermulti/count/PBMC_10K_CMV/outs/vdj_t/all_contig_annotations.json", "cellrangermulti/mkgtf", "cellrangermulti/mkgtf/Homo_sapiens.GRCh38.dna.chromosome.14_genes.filtered.gtf", "cellrangermulti/mkref", @@ -913,6 +942,9 @@ "cellrangermulti/mkvdjref/vdj_reference/reference.json", "cellrangermulti/mtx_conversions", "cellrangermulti/mtx_conversions/4PLEX_HUMAN", + "cellrangermulti/mtx_conversions/4PLEX_HUMAN/4PLEX_HUMAN_filtered_matrix.h5ad", + "cellrangermulti/mtx_conversions/4PLEX_HUMAN/4PLEX_HUMAN_filtered_matrix.sce.rds", + "cellrangermulti/mtx_conversions/4PLEX_HUMAN/4PLEX_HUMAN_filtered_matrix.seurat.rds", "cellrangermulti/mtx_conversions/4PLEX_HUMAN/4PLEX_HUMAN_raw_matrix.h5ad", "cellrangermulti/mtx_conversions/4PLEX_HUMAN/4PLEX_HUMAN_raw_matrix.sce.rds", "cellrangermulti/mtx_conversions/4PLEX_HUMAN/4PLEX_HUMAN_raw_matrix.seurat.rds", @@ -945,6 +977,9 @@ "cellrangermulti/mtx_conversions/PBMC_10K/PBMC_10K_raw_matrix.sce.rds", "cellrangermulti/mtx_conversions/PBMC_10K/PBMC_10K_raw_matrix.seurat.rds", "cellrangermulti/mtx_conversions/PBMC_10K_CMO", + "cellrangermulti/mtx_conversions/PBMC_10K_CMO/PBMC_10K_CMO_filtered_matrix.h5ad", + "cellrangermulti/mtx_conversions/PBMC_10K_CMO/PBMC_10K_CMO_filtered_matrix.sce.rds", + "cellrangermulti/mtx_conversions/PBMC_10K_CMO/PBMC_10K_CMO_filtered_matrix.seurat.rds", "cellrangermulti/mtx_conversions/PBMC_10K_CMO/PBMC_10K_CMO_raw_matrix.h5ad", "cellrangermulti/mtx_conversions/PBMC_10K_CMO/PBMC_10K_CMO_raw_matrix.sce.rds", "cellrangermulti/mtx_conversions/PBMC_10K_CMO/PBMC_10K_CMO_raw_matrix.seurat.rds", @@ -952,10 +987,16 @@ "cellrangermulti/mtx_conversions/PBMC_10K_CMO_PBMCs_human_1/PBMC_10K_CMO_PBMCs_human_1_filtered_matrix.h5ad", "cellrangermulti/mtx_conversions/PBMC_10K_CMO_PBMCs_human_1/PBMC_10K_CMO_PBMCs_human_1_filtered_matrix.sce.rds", "cellrangermulti/mtx_conversions/PBMC_10K_CMO_PBMCs_human_1/PBMC_10K_CMO_PBMCs_human_1_filtered_matrix.seurat.rds", + "cellrangermulti/mtx_conversions/PBMC_10K_CMO_PBMCs_human_1/PBMC_10K_CMO_PBMCs_human_1_raw_matrix.h5ad", + "cellrangermulti/mtx_conversions/PBMC_10K_CMO_PBMCs_human_1/PBMC_10K_CMO_PBMCs_human_1_raw_matrix.sce.rds", + "cellrangermulti/mtx_conversions/PBMC_10K_CMO_PBMCs_human_1/PBMC_10K_CMO_PBMCs_human_1_raw_matrix.seurat.rds", "cellrangermulti/mtx_conversions/PBMC_10K_CMO_PBMCs_human_2", "cellrangermulti/mtx_conversions/PBMC_10K_CMO_PBMCs_human_2/PBMC_10K_CMO_PBMCs_human_2_filtered_matrix.h5ad", "cellrangermulti/mtx_conversions/PBMC_10K_CMO_PBMCs_human_2/PBMC_10K_CMO_PBMCs_human_2_filtered_matrix.sce.rds", "cellrangermulti/mtx_conversions/PBMC_10K_CMO_PBMCs_human_2/PBMC_10K_CMO_PBMCs_human_2_filtered_matrix.seurat.rds", + "cellrangermulti/mtx_conversions/PBMC_10K_CMO_PBMCs_human_2/PBMC_10K_CMO_PBMCs_human_2_raw_matrix.h5ad", + "cellrangermulti/mtx_conversions/PBMC_10K_CMO_PBMCs_human_2/PBMC_10K_CMO_PBMCs_human_2_raw_matrix.sce.rds", + "cellrangermulti/mtx_conversions/PBMC_10K_CMO_PBMCs_human_2/PBMC_10K_CMO_PBMCs_human_2_raw_matrix.seurat.rds", "cellrangermulti/mtx_conversions/PBMC_10K_CMV", 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"Pancreas_BC4_filtered_matrix.sce.rds:md5,7d18f78c68f7c995b724ae3ba95ea862", - "Pancreas_BC4_filtered_matrix.seurat.rds:md5,98eef51fc0c34fa1e055b04c5c92d2f0", + "Pancreas_BC4_filtered_matrix.h5ad:md5,09c9498c4e0620be89b60d9534bd5135", + "Pancreas_BC4_filtered_matrix.sce.rds:md5,5f0b30f194252b9eb3ba8b0526b89843", + "Pancreas_BC4_filtered_matrix.seurat.rds:md5,8c04395c01e9f4c57c606ed5c360ff56", "Pancreas_BC4_raw_matrix.h5ad:md5,227d5886282d58e0c6b8d6adc9ef94d0", "Pancreas_BC4_raw_matrix.sce.rds:md5,4af114f068fc9bab8cceb3f25a9b6d9a", "Pancreas_BC4_raw_matrix.seurat.rds:md5,7f972f40b05824a3cff5449a8f9f8b61", @@ -1244,26 +1321,26 @@ ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-10-23T19:20:06.700106749" + "timestamp": "2025-11-20T16:25:55.242388145" }, "test-dataset_cellrangermulti_aligner_rat": { "content": [ - 32, + 34, { "CELLRANGER_MKGTF": { - "cellranger": "9.0.1" + "cellranger": "10.0.0" }, "CELLRANGER_MKREF": { - "cellranger": "9.0.1" + "cellranger": "10.0.0" }, "CELLRANGER_MKVDJREF": { - "cellranger": "9.0.1" + "cellranger": "10.0.0" }, "CELLRANGER_MULTI": { - "cellranger": "9.0.1 " + "cellranger": "cellranger 10.0.0 " }, "FASTQC": { "fastqc": "0.12.1" @@ -1287,320 +1364,322 @@ "cellrangermulti/count/10k_Wistar_Rat", "cellrangermulti/count/10k_Wistar_Rat/outs", "cellrangermulti/count/10k_Wistar_Rat/outs/config.csv", - "cellrangermulti/count/10k_Wistar_Rat/outs/multi", - "cellrangermulti/count/10k_Wistar_Rat/outs/multi/count", - "cellrangermulti/count/10k_Wistar_Rat/outs/multi/count/raw_cloupe.cloupe", - "cellrangermulti/count/10k_Wistar_Rat/outs/multi/count/raw_feature_bc_matrix", - "cellrangermulti/count/10k_Wistar_Rat/outs/multi/count/raw_feature_bc_matrix.h5", - "cellrangermulti/count/10k_Wistar_Rat/outs/multi/count/raw_feature_bc_matrix/barcodes.tsv.gz", - "cellrangermulti/count/10k_Wistar_Rat/outs/multi/count/raw_feature_bc_matrix/features.tsv.gz", - 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"cellrangermulti/count/10k_Wistar_Rat/outs/unassigned_alignments.bam", + "cellrangermulti/count/10k_Wistar_Rat/outs/unassigned_alignments.bam.bai", "cellrangermulti/mkgtf", "cellrangermulti/mkgtf/Rattus_norvegicus.GRCr8.dna.primary_assembly.6_genes.filtered.gtf", "cellrangermulti/mkref", @@ -1635,6 +1714,9 @@ "cellrangermulti/mkvdjref/vdj_reference/reference.json", "cellrangermulti/mtx_conversions", "cellrangermulti/mtx_conversions/10k_Wistar_Rat", + "cellrangermulti/mtx_conversions/10k_Wistar_Rat/10k_Wistar_Rat_filtered_matrix.h5ad", + "cellrangermulti/mtx_conversions/10k_Wistar_Rat/10k_Wistar_Rat_filtered_matrix.sce.rds", + "cellrangermulti/mtx_conversions/10k_Wistar_Rat/10k_Wistar_Rat_filtered_matrix.seurat.rds", "cellrangermulti/mtx_conversions/10k_Wistar_Rat/10k_Wistar_Rat_raw_matrix.h5ad", "cellrangermulti/mtx_conversions/10k_Wistar_Rat/10k_Wistar_Rat_raw_matrix.sce.rds", "cellrangermulti/mtx_conversions/10k_Wistar_Rat/10k_Wistar_Rat_raw_matrix.seurat.rds", @@ -1760,33 +1842,36 @@ "pipeline_info/nf_core_scrnaseq_software_mqc_versions.yml" ], [ - "barcodes.tsv.gz:md5,b8392e06463e9b5d87528c2898539540", + "barcodes.tsv.gz:md5,2134778c7211b79c1a9e12db033b76d6", "features.tsv.gz:md5,b55feb80459101d27ee0b2580af0d53c", - "matrix.mtx.gz:md5,215bf0efebc1cb89ec754bf186c80909", + "matrix.mtx.gz:md5,9547b96c45d64283d5ee65243f20ac3a", "barcodes.tsv.gz:md5,5916dd03abc1ec3c621ac62e090ddbfb", "features.tsv.gz:md5,b55feb80459101d27ee0b2580af0d53c", - "matrix.mtx.gz:md5,00011c41088ca6b405db7becc0c81682", + "matrix.mtx.gz:md5,638b438dbfa0a0b408991fb4ad0f5392", "barcodes.tsv.gz:md5,963fb610c6e379c9285314ae07cb41be", "features.tsv.gz:md5,b55feb80459101d27ee0b2580af0d53c", - "matrix.mtx.gz:md5,89cdcd0c7ac87b0706e07022e0cb152b", + "matrix.mtx.gz:md5,a5ad8c3557cb905b758f65074ee52625", "barcodes.tsv.gz:md5,8973bb4c7b5c211dd1ffe003502166c0", "features.tsv.gz:md5,b55feb80459101d27ee0b2580af0d53c", - "matrix.mtx.gz:md5,bec72997f928ded91d60e6fb30945efb", + "matrix.mtx.gz:md5,d7c0136e6ed56a8735fefcea8db4ce2c", "barcodes.tsv.gz:md5,4d1716fb5b1aae766e58e8ad971040a6", "features.tsv.gz:md5,b55feb80459101d27ee0b2580af0d53c", - "matrix.mtx.gz:md5,e4ef811570097ad41a229ec0ec6e612b", + "matrix.mtx.gz:md5,85479c643d93e5293c0dd9c00d5de243", "barcodes.tsv.gz:md5,b5b2c8ac0a8f655ca53397dd337bca27", "features.tsv.gz:md5,b55feb80459101d27ee0b2580af0d53c", - "matrix.mtx.gz:md5,22833228f201dd010b6c40e035a42cab", + "matrix.mtx.gz:md5,a0f540683f76133c70910807d328e836", "barcodes.tsv.gz:md5,b6fae74b4c42d097b2325462729c795b", "features.tsv.gz:md5,b55feb80459101d27ee0b2580af0d53c", - "matrix.mtx.gz:md5,af11682ebb2ef03eb8468206bb576331", + "matrix.mtx.gz:md5,92c402a8e3cf9023102fa7d63fe06eda", "barcodes.tsv.gz:md5,bb62ec4602c7579b20adf5ad2b4124d2", "features.tsv.gz:md5,b55feb80459101d27ee0b2580af0d53c", - "matrix.mtx.gz:md5,ac8bd7e83e9fde9d47454b323bed36d6", + "matrix.mtx.gz:md5,c8cad4ff5a074649779e9a9982be55d9", "barcodes.tsv.gz:md5,e9a3e5323176ac3dfcad090f4a17d788", "features.tsv.gz:md5,b55feb80459101d27ee0b2580af0d53c", - "matrix.mtx.gz:md5,aebb9ff23ed62a737b560f1fd1d1162d", + "matrix.mtx.gz:md5,c622cc212a41a3f3f789c382ac9708a3", + "barcodes.tsv.gz:md5,b8392e06463e9b5d87528c2898539540", + "features.tsv.gz:md5,b55feb80459101d27ee0b2580af0d53c", + "matrix.mtx.gz:md5,4fea195b49f8ef618e6708071e955a30", "Rattus_norvegicus.GRCr8.dna.primary_assembly.6_genes.filtered.gtf:md5,1c0c684e8bc3407d13cac54728c660cd", "genome.fa:md5,4314b5b9035bda1101636a10159680a3", "genome.fa.fai:md5,abbcafd221163873f0519fa7d0563af8", @@ -1805,8 +1890,11 @@ "sjdbList.fromGTF.out.tab:md5,3cb30688675c43e4e1dd605d6222e86e", "sjdbList.out.tab:md5,47f3998d3b00a1cbe34d9892771c3134", "transcriptInfo.tab:md5,213158051b61081ed7bd8f39c0324072", - "versions.yml:md5,7f4adb1e901d6610e40f18a6b7c1dc89", + "versions.yml:md5,871d12d497419f681e7a60fd1af17dba", "regions.fa:md5,be846142763972b29bbf65ff7e1406ee", + "10k_Wistar_Rat_filtered_matrix.h5ad:md5,19a1654b5197254a71d57c77903a9af5", + "10k_Wistar_Rat_filtered_matrix.sce.rds:md5,e1904cd2ab64b598214f5fcfccfdc498", + "10k_Wistar_Rat_filtered_matrix.seurat.rds:md5,94d0c5f59e18fa44bc588242bcbc4bde", "10k_Wistar_Rat_raw_matrix.h5ad:md5,b72f3744ea8ade292165de67491694ba", "10k_Wistar_Rat_raw_matrix.sce.rds:md5,170343f922c2b73f137fff406e1316c3", "10k_Wistar_Rat_raw_matrix.seurat.rds:md5,be37ed0efb84a22909063388c54c4154", @@ -1849,9 +1937,9 @@ ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-10-23T19:49:18.434722245" + "timestamp": "2025-11-20T16:41:39.841222271" } } \ No newline at end of file