Merge pull request #276 from nf-core/247-support-for-10x-ffpe-scrna

Adding cellrangermulti subworkflow

.github/workflows/ci.yml

@@ -33,7 +33,7 @@ jobs:
         NXF_VER:
           - "23.04.0"
           - "latest-everything"
-        profile: ["alevin", "cellranger", "kallisto", "star"]
+        profile: ["alevin", "cellranger", "cellrangermulti", "kallisto", "star"]
 
     steps:
       - name: Disk space cleanup

CHANGELOG.md

@@ -3,6 +3,10 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## v2.7.0dev
+
+- Add cellranger multi subworkflow ([#247](https://github.com/nf-core/scrnaseq/issues/247))
+
 ## v2.6.0 - 2024-04-16
 
 - Update cellranger to v8.0.0 ([#317](https://github.com/nf-core/scrnaseq/pull/317))

assets/EMPTY

@@ -0,0 +1 @@
+

assets/cellranger_barcodes_samplesheet.csv

@@ -0,0 +1,7 @@
+sample,multiplexed_sample_id,probe_barcode_ids,cmo_ids,description
+PBMC_10K_CMO,PBMC_10K_CMO_PBMCs_human_1,,CMO301,PBMCs_human_1
+PBMC_10K_CMO,PBMC_10K_CMO_PBMCs_human_2,,CMO302,PBMCs_human_2
+4PLEX_HUMAN,Liver_BC1,BC001,,Healthy liver dissociated using the Miltenyi FFPE Tissue Dissociation Kit
+4PLEX_HUMAN,Ovarian_BC2,BC002,,Ovarian cancer dissociated using the Miltenyi FFPE Dissociation Kit
+4PLEX_HUMAN,Colorectal_BC3,BC003,,Colorectal cancer dissociated using the Miltenyi FFPE Dissociation Kit
+4PLEX_HUMAN,Pancreas_BC4,BC004,,Healthy pancreas dissociated using the Miltenyi FFPE Tissue Dissociation Kit

assets/cellrangermulti_samplesheet.csv

@@ -0,0 +1,13 @@
+sample,fastq_1,fastq_2,feature_type,expected_cells
+PBMC_10K,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc/fastqs/5gex/5gex/subsampled_sc5p_v2_hs_PBMC_10k_5gex_S1_L001_R1_001.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc/fastqs/5gex/5gex/subsampled_sc5p_v2_hs_PBMC_10k_5gex_S1_L001_R2_001.fastq.gz,gex,1000
+PBMC_10K,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc/fastqs/bcell/subsampled_sc5p_v2_hs_PBMC_10k_b_S1_L001_R1_001.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc/fastqs/bcell/subsampled_sc5p_v2_hs_PBMC_10k_b_S1_L001_R2_001.fastq.gz,vdj,1000
+PBMC_10K,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc/fastqs/5gex/5fb/subsampled_sc5p_v2_hs_PBMC_10k_5fb_S1_L001_R1_001.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc/fastqs/5gex/5fb/subsampled_sc5p_v2_hs_PBMC_10k_5fb_S1_L001_R2_001.fastq.gz,ab,1000
+PBMC_10K_CMO,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc_cmo/fastqs/gex_1/subsampled_SC3_v3_NextGem_DI_CellPlex_Human_PBMC_10K_1_gex_S2_L001_R1_001.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc_cmo/fastqs/gex_1/subsampled_SC3_v3_NextGem_DI_CellPlex_Human_PBMC_10K_1_gex_S2_L001_R2_001.fastq.gz,gex,1000
+PBMC_10K_CMO,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc_cmo/fastqs/cmo/subsampled_SC3_v3_NextGem_DI_CellPlex_Human_PBMC_10K_1_multiplexing_capture_S1_L001_R1_001.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc_cmo/fastqs/cmo/subsampled_SC3_v3_NextGem_DI_CellPlex_Human_PBMC_10K_1_multiplexing_capture_S1_L001_R2_001.fastq.gz,cmo,1000
+PBMC_10K_CMV,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/10xgenomics/cellranger/5k_cmvpos_tcells/fastqs/gex_1/subsampled_5k_human_antiCMV_T_TBNK_connect_GEX_1_S1_L001_R1_001.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/10xgenomics/cellranger/5k_cmvpos_tcells/fastqs/gex_1/subsampled_5k_human_antiCMV_T_TBNK_connect_GEX_1_S1_L001_R2_001.fastq.gz,gex,1000
+PBMC_10K_CMV,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/10xgenomics/cellranger/5k_cmvpos_tcells/fastqs/ab/subsampled_5k_human_antiCMV_T_TBNK_connect_AB_S2_L004_R1_001.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/10xgenomics/cellranger/5k_cmvpos_tcells/fastqs/ab/subsampled_5k_human_antiCMV_T_TBNK_connect_AB_S2_L004_R2_001.fastq.gz,ab,1000
+PBMC_10K_CMV,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/10xgenomics/cellranger/5k_cmvpos_tcells/fastqs/vdj/subsampled_5k_human_antiCMV_T_TBNK_connect_VDJ_S1_L001_R1_001.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/10xgenomics/cellranger/5k_cmvpos_tcells/fastqs/vdj/subsampled_5k_human_antiCMV_T_TBNK_connect_VDJ_S1_L001_R2_001.fastq.gz,vdj,1000
+4PLEX_HUMAN,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/10xgenomics/cellranger/4plex_scFFPE/4plex_human_liver_colorectal_ovarian_panc_scFFPE_multiplex_S1_L001_R1_001.subsampled.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/10xgenomics/cellranger/4plex_scFFPE/4plex_human_liver_colorectal_ovarian_panc_scFFPE_multiplex_S1_L001_R2_001.subsampled.fastq.gz,gex,
+4PLEX_HUMAN,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/10xgenomics/cellranger/4plex_scFFPE/4plex_human_liver_colorectal_ovarian_panc_scFFPE_multiplex_S1_L002_R1_001.subsampled.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/10xgenomics/cellranger/4plex_scFFPE/4plex_human_liver_colorectal_ovarian_panc_scFFPE_multiplex_S1_L002_R2_001.subsampled.fastq.gz,gex,
+4PLEX_HUMAN,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/10xgenomics/cellranger/4plex_scFFPE/4plex_human_liver_colorectal_ovarian_panc_scFFPE_multiplex_S1_L003_R1_001.subsampled.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/10xgenomics/cellranger/4plex_scFFPE/4plex_human_liver_colorectal_ovarian_panc_scFFPE_multiplex_S1_L003_R2_001.subsampled.fastq.gz,gex,
+4PLEX_HUMAN,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/10xgenomics/cellranger/4plex_scFFPE/4plex_human_liver_colorectal_ovarian_panc_scFFPE_multiplex_S1_L004_R1_001.subsampled.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/10xgenomics/cellranger/4plex_scFFPE/4plex_human_liver_colorectal_ovarian_panc_scFFPE_multiplex_S1_L004_R2_001.subsampled.fastq.gz,gex,

assets/fb_reference.csv

@@ -0,0 +1,12 @@
+id,name,read,pattern,sequence,feature_type
+CD3,CD3,R2,^NNNNNNNNNN(BC)NNNNNNNNN,CTCATTGTAACTCCT,Antibody Capture
+CD4,CD4,R2,^NNNNNNNNNN(BC)NNNNNNNNN,TGTTCCCGCTCAACT,Antibody Capture
+CD8,CD8,R2,^NNNNNNNNNN(BC)NNNNNNNNN,GCGCAACTTGATGAT,Antibody Capture
+CD11c,CD11c,R2,^NNNNNNNNNN(BC)NNNNNNNNN,TACGCCTATAACTTG,Antibody Capture
+CD14,CD14,R2,^NNNNNNNNNN(BC)NNNNNNNNN,TCTCAGACCTCCGTA,Antibody Capture
+CD16,CD16,R2,^NNNNNNNNNN(BC)NNNNNNNNN,AAGTTCACTCTTTGC,Antibody Capture
+CD19,CD19,R2,^NNNNNNNNNN(BC)NNNNNNNNN,CTGGGCAATTACTCG,Antibody Capture
+CD56,CD56,R2,^NNNNNNNNNN(BC)NNNNNNNNN,TCCTTTCCTGATAGG,Antibody Capture
+CD45,CD45,R2,^NNNNNNNNNN(BC)NNNNNNNNN,TCCCTTGCGATTTAC,Antibody Capture
+IgG1,IgG1_control_TotalSeqC,R2,^NNNNNNNNNN(BC)NNNNNNNNN,GCCGGACGACATTAA,Antibody Capture
+A0201_NLVPMVATV_CMV_TCR-1,NLVPMVATV_CMV_TCR-1,R2,^NNNNNNNNNN(BC)NNNNNNNNN,GGCCTCGGTCCTAGG,Antibody Capture