Adding cellrangermulti subworkflow

[fmalmeida]

Close #247 Close #313

PR checklist

• [ ] This comment contains a description of changes (with reason).
• [ ] If you've fixed a bug or added code that should be tested, add tests!
• [ ] If you've added a new tool - have you followed the pipeline conventions in the contribution docs
• [ ] If necessary, also make a PR on the nf-core/scrnaseq branch on the nf-core/test-datasets repository.
• [ ] Make sure your code lints (nf-core lint).
• [ ] Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• [ ] Usage Documentation in docs/usage.md is updated.
• [ ] Output Documentation in docs/output.md is updated.
• [ ] CHANGELOG.md is updated.
• [ ] README.md is updated (including new tool citations and authors/contributors).

Context

Hi guys,

Although not finished yet because it would still required updating the parameters schema, defaults and documentation, I am already opening the PR so we can all take a look at it and discuss any modifications required before merging and also, give it a round of tests and define how we want some parameters to be.

I used the templates provided by @klkeys

Usage context

samplesheet To use it, samplesheet requires an additional parameter so that we can properly mix the different feature types given per sample.

sample,fastq_1,fastq_2,feature_type,protocol,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,SC5P-PE,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,SC5P-PE,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,SC5P-PE,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,SC3Pv3,1000
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,SC3Pv3,1000
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,SC5P-R2,1000
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,SC5P-R2,1000
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,SC5P-R2,1000

Supporting files

Right now, all the supporting files have been added as parameters, for example, cmo_barcode_csv, beam_antigen_csv, etc. .... which means they will work in a dataset manner, being the same for everything given in the samplesheet, instead of samplesheet base if they were added as columns in the samplesheet.

My main question here is, what should it be the desired approach?

Other stuff Of course there might still have things to clear or finish that I might have overlooked since there is quite a lot on it, so, I request your help on spotting it.

testing case required the full genomes from ensembl, otherwise, the analysis using VDJ was failling.