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Fix: Update Cellranger/multi to reinclude functionality from previous PR update #12152

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Fix: Update Cellranger/multi to reinclude functionality from previous PR update #12152

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88f0447
Update code for missing flags
mahesh-panchal Jun 23, 2026
824202b
Update meta
mahesh-panchal Jun 23, 2026
256654d
Update test input channels
mahesh-panchal Jun 23, 2026
b241db3
Remove flag
mahesh-panchal Jun 23, 2026
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78 changes: 51 additions & 27 deletions modules/nf-core/cellranger/multi/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -6,12 +6,12 @@ process CELLRANGER_MULTI {

input:
val meta
tuple val(meta2) , path (gex_fastqs , stageAs: "fastqs/gex/fastq_???/*") , val(gex_options)
tuple val(meta3) , path (vdj_fastqs , stageAs: "fastqs/vdj/fastq_???/*")
tuple val(meta4) , path (ab_fastqs , stageAs: "fastqs/ab/fastq_???/*")
tuple val(meta5) , path (beam_fastqs , stageAs: "fastqs/beam/fastq_???/*")
tuple val(meta6) , path (cmo_fastqs , stageAs: "fastqs/cmo/fastq_???/*")
tuple val(meta7) , path (crispr_fastqs, stageAs: "fastqs/crispr/fastq_???/*")
tuple val(meta2) , path (gex_fastqs , stageAs: "fastqs/gex/fastq_???/*") , val(gex_options)
tuple val(meta3) , path (vdj_fastqs , stageAs: "fastqs/vdj/fastq_???/*") , val(vdj_options)
tuple val(meta4) , path (ab_fastqs , stageAs: "fastqs/ab/fastq_???/*") , val(ab_options)
tuple val(meta5) , path (beam_fastqs , stageAs: "fastqs/beam/fastq_???/*") , val(beam_options)
tuple val(meta6) , path (cmo_fastqs , stageAs: "fastqs/cmo/fastq_???/*") , val(cmo_options)
tuple val(meta7) , path (crispr_fastqs, stageAs: "fastqs/crispr/fastq_???/*"), val(crispr_options)
path gex_reference , stageAs: "references/gex/*"
path gex_frna_probeset , stageAs: "references/gex/probeset/*"
path gex_targetpanel , stageAs: "references/gex/targetpanel/*"
Expand Down Expand Up @@ -66,28 +66,40 @@ process CELLRANGER_MULTI {
gex_section << "reference,\$PWD/${gex_reference.name}"
if (gex_frna_probeset) gex_section << "probe-set,\$PWD/${gex_frna_probeset.name}"

// GEX options from a dedicated input channel
def gex_has_opts = gex_options ?: [:]
def chemistry = gex_has_opts.containsKey("chemistry") ? gex_has_opts["chemistry"] : "auto"
gex_section << "chemistry,${chemistry}"

if (gex_has_opts.containsKey("expect-cells")) {
gex_section << "expect-cells,${gex_has_opts["expect-cells"]}"
// GEX options forwarded from the gex_options input map
['filter-probes', 'r1-length', 'r2-length', 'chemistry', 'expect-cells', 'force-cells',
'no-secondary', 'check-library-compatibility', 'no-target-umi-filter', 'include-introns'].each { key ->
if (gex_options?.containsKey(key)) gex_section << "${key},${gex_options[key]}"
}

def create_bam = gex_has_opts.containsKey("create-bam") ? gex_has_opts["create-bam"] : "true"
gex_section << "create-bam,${create_bam}"
// create-bam defaults to true if not specified
gex_section << "create-bam,${gex_options?.get('create-bam') ?: 'true'}"

if (gex_targetpanel) {
gex_section << "target-panel,\$PWD/${gex_targetpanel.name}"
}

// CMO-related settings that live inside the [gene-expression] section
if (has_cmo) {
if (cmo_options?.containsKey('min-assignment-confidence')) {
gex_section << "min-assignment-confidence,${cmo_options['min-assignment-confidence']}"
}
if (cmo_reference) gex_section << "cmo-set,\$PWD/${cmo_reference.name}"
if (cmo_barcode_assignment) gex_section << "barcode-sample-assignment,\$PWD/${cmo_barcode_assignment.name}"
}
}

// Build [feature] section
def fb_section = []
if (has_ab || has_crispr) {
if (has_ab || has_crispr || has_beam) {
fb_section << '[feature]'
fb_section << 'reference,\$PWD/fb_reference_copy.csv'
if (has_ab || has_crispr) fb_section << 'reference,\$PWD/fb_reference_copy.csv'
if (has_beam && beam_antigen_panel) fb_section << "reference,\$PWD/${beam_antigen_panel.name}"

// r1/r2-length from ab_options takes priority over crispr_options
def fb_opts = has_ab ? ab_options : (has_crispr ? crispr_options : null)
if (fb_opts?.containsKey('r1-length')) fb_section << "r1-length,${fb_opts['r1-length']}"
if (fb_opts?.containsKey('r2-length')) fb_section << "r2-length,${fb_opts['r2-length']}"
}

// Build [vdj] section
Expand All @@ -98,6 +110,8 @@ process CELLRANGER_MULTI {
if (vdj_primer_index) {
vdj_section << "inner-enrichment-primers,\$PWD/${vdj_primer_index.name}"
}
if (vdj_options?.containsKey('r1-length')) vdj_section << "r1-length,${vdj_options['r1-length']}"
if (vdj_options?.containsKey('r2-length')) vdj_section << "r2-length,${vdj_options['r2-length']}"
}

// Build [libraries] section
Expand Down Expand Up @@ -129,25 +143,35 @@ process CELLRANGER_MULTI {
config_lines << '[samples]'
config_lines << ocm_barcodes.text.trim()
}
if (has_beam) {
config_lines << '[antigen-specificity]'
config_lines << beam_control_panel.text.trim()
}
def config_content = config_lines.findAll { line -> line }.join('\n ')
"""
#
# Rename FASTQs to Cell Ranger naming convention
# Maintains R1/R2 pairing order by processing directories sequentially
# Output pattern: \${prefix}_S1_L001_R1_001.fastq.gz, L002_R1_001.fastq.gz, etc.
# Symlink FASTQs into fastq_all/, maintaining R1/R2 lane-pairing order.
# skip_renaming=false (default): rename to Cell Ranger convention \${prefix}_S1_L00N_R[12]_001.fastq.gz
# skip_renaming=true: keep original filenames as-is
#
mkdir -p fastq_all/{gex,vdj,ab,beam,cmo,crispr}

for modality in gex vdj ab beam cmo crispr; do
lane=1
while IFS= read -r -d '' r1_dir && IFS= read -r -d '' r2_dir; do
r1=\$(find "\${r1_dir}" -maxdepth 1 -name "*_R1_*.fastq.gz" | head -1)
r2=\$(find "\${r2_dir}" -maxdepth 1 -name "*_R2_*.fastq.gz" | head -1)

[ -z "\${r1}" ] || [ -z "\${r2}" ] && continue

ln -sf "\$(readlink -f "\${r1}")" "fastq_all/\${modality}/${prefix}_S1_L\$(printf %03d \${lane})_R1_001.fastq.gz"
ln -sf "\$(readlink -f "\${r2}")" "fastq_all/\${modality}/${prefix}_S1_L\$(printf %03d \${lane})_R2_001.fastq.gz"
if [ "${skip_renaming}" = "true" ]; then
r1=\$(find "\${r1_dir}" -maxdepth 1 -name "*.fastq.gz" | head -1)
r2=\$(find "\${r2_dir}" -maxdepth 1 -name "*.fastq.gz" | head -1)
[ -z "\${r1}" ] || [ -z "\${r2}" ] && continue
ln -sf "\$(readlink -f "\${r1}")" "fastq_all/\${modality}/\$(basename "\${r1}")"
ln -sf "\$(readlink -f "\${r2}")" "fastq_all/\${modality}/\$(basename "\${r2}")"
else
r1=\$(find "\${r1_dir}" -maxdepth 1 -name "*_R1_*.fastq.gz" | head -1)
r2=\$(find "\${r2_dir}" -maxdepth 1 -name "*_R2_*.fastq.gz" | head -1)
[ -z "\${r1}" ] || [ -z "\${r2}" ] && continue
ln -sf "\$(readlink -f "\${r1}")" "fastq_all/\${modality}/${prefix}_S1_L\$(printf %03d \${lane})_R1_001.fastq.gz"
ln -sf "\$(readlink -f "\${r2}")" "fastq_all/\${modality}/${prefix}_S1_L\$(printf %03d \${lane})_R2_001.fastq.gz"
fi
lane=\$((lane + 1))
done < <(find fastqs/\${modality} -maxdepth 1 -type d -name "fastq_*" | sort | xargs -n1 printf '%s\\0')
done
Expand Down
30 changes: 28 additions & 2 deletions modules/nf-core/cellranger/multi/meta.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -42,8 +42,10 @@ input:
- gex_options:
type: map
description: |
Optional Cell Ranger gene expression section options.
Supported keys include chemistry, expect-cells, and create-bam.
Optional Cell Ranger gene expression section options as a Map.
Supported keys: filter-probes, r1-length, r2-length, chemistry, expect-cells,
force-cells, no-secondary, check-library-compatibility, no-target-umi-filter,
include-introns, create-bam (defaults to true if not set).
- - meta3:
type: map
description: |
Expand All @@ -54,6 +56,11 @@ input:
pattern: "*.fastq.gz"
ontologies:
- edam: http://edamontology.org/format_3989
- vdj_options:
type: map
description: |
Optional Cell Ranger VDJ section options as a Map.
Supported keys: r1-length, r2-length.
- - meta4:
type: map
description: |
Expand All @@ -64,6 +71,11 @@ input:
pattern: "*.fastq.gz"
ontologies:
- edam: http://edamontology.org/format_3989
- ab_options:
type: map
description: |
Optional Cell Ranger feature section options for Antibody Capture as a Map.
Pass null to disable this modality. Supported keys: r1-length, r2-length.
- - meta5:
type: map
description: |
Expand All @@ -74,6 +86,10 @@ input:
pattern: "*.fastq.gz"
ontologies:
- edam: http://edamontology.org/format_3989
- beam_options:
type: map
description: |
Optional Cell Ranger BEAM section options as a Map. Reserved for future use.
- - meta6:
type: map
description: |
Expand All @@ -84,6 +100,11 @@ input:
pattern: "*.fastq.gz"
ontologies:
- edam: http://edamontology.org/format_3989
- cmo_options:
type: map
description: |
Optional Cell Ranger CMO section options as a Map.
Supported keys: min-assignment-confidence.
- - meta7:
type: map
description: |
Expand All @@ -94,6 +115,11 @@ input:
pattern: "*.fastq.gz"
ontologies:
- edam: http://edamontology.org/format_3989
- crispr_options:
type: map
description: |
Optional Cell Ranger feature section options for CRISPR Guide Capture as a Map.
Pass null to disable this modality. Supported keys: r1-length, r2-length.
- gex_reference:
type: directory
description: Folder containing Cellranger gene expression reference. Can also
Expand Down
82 changes: 41 additions & 41 deletions modules/nf-core/cellranger/multi/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -167,12 +167,12 @@ nextflow_process {
// create empty channels to fill unused cellranger multi arguments
// fastqs need a [ meta, ref ] structure
// references just need a path
ch_gex_fastqs = [ [:], [], [] ]
ch_vdj_fastqs = [ [:], [] ]
ch_ab_fastqs = [ [:], [] ]
ch_beam_fastqs = [ [:], [] ]
ch_cmo_fastqs = [ [:], [] ]
ch_crispr_fastqs = [ [:], [] ]
ch_gex_fastqs = [ [:], [], [:] ]
ch_vdj_fastqs = [ [:], [], [:] ]
ch_ab_fastqs = [ [:], [], [:] ]
ch_beam_fastqs = [ [:], [], [:] ]
ch_cmo_fastqs = [ [:], [], [:] ]
ch_crispr_fastqs = [ [:], [], [:] ]
ch_gex_frna_probeset = []
ch_gex_targetpanel = []
ch_vdj_primer_index = []
Expand All @@ -192,10 +192,10 @@ nextflow_process {
ch_vdj_reference = Channel.of( vdj_reference )
ch_bcell_fastqs_10k_pbmc = Channel.of( bcell_fastqs_10k_pbmc )
.collect()
.map { reads -> [ [ id:bcell_fastq_samplename_10k_pbmc ], reads ] }
.map { reads -> [ [ id:bcell_fastq_samplename_10k_pbmc ], reads, [:] ] }
ch_ab_fastqs_10k_pbmc = Channel.of( ab_fastqs_10k_pbmc )
.collect()
.map { reads -> [ [ id:fivepab_fastq_samplename_10k_pbmc ], reads ] }
.map { reads -> [ [ id:fivepab_fastq_samplename_10k_pbmc ], reads, [:] ] }
ch_ab_reference_10k_pbmc = Channel.of( fb_reference_10k_pbmc )

//
Expand Down Expand Up @@ -388,12 +388,12 @@ nextflow_process {
// create empty channels to fill unused cellranger multi arguments
// fastqs need a [ meta, ref ] structure
// references just need a path
ch_gex_fastqs = [ [:], [], [] ]
ch_vdj_fastqs = [ [:], [] ]
ch_ab_fastqs = [ [:], [] ]
ch_beam_fastqs = [ [:], [] ]
ch_cmo_fastqs = [ [:], [] ]
ch_crispr_fastqs = [ [:], [] ]
ch_gex_fastqs = [ [:], [], [:] ]
ch_vdj_fastqs = [ [:], [], [:] ]
ch_ab_fastqs = [ [:], [], [:] ]
ch_beam_fastqs = [ [:], [], [:] ]
ch_cmo_fastqs = [ [:], [], [:] ]
ch_crispr_fastqs = [ [:], [], [:] ]
ch_gex_frna_probeset = []
ch_gex_targetpanel = []
ch_vdj_primer_index = []
Expand All @@ -413,10 +413,10 @@ nextflow_process {
ch_vdj_reference = Channel.of( vdj_reference )
ch_bcell_fastqs_10k_pbmc = Channel.of( bcell_fastqs_10k_pbmc )
.collect()
.map { reads -> [ [ id:bcell_fastq_samplename_10k_pbmc ], reads ] }
.map { reads -> [ [ id:bcell_fastq_samplename_10k_pbmc ], reads, [:] ] }
ch_ab_fastqs_10k_pbmc = Channel.of( ab_fastqs_10k_pbmc )
.collect()
.map { reads -> [ [ id:fivepab_fastq_samplename_10k_pbmc ], reads ] }
.map { reads -> [ [ id:fivepab_fastq_samplename_10k_pbmc ], reads, [:] ] }
ch_ab_reference_10k_pbmc = Channel.of( fb_reference_10k_pbmc )

ch_gex_fastqs_10k_pbmc_cmo = Channel.of( threepgex_fastqs_10k_pbmc_cmo )
Expand All @@ -425,7 +425,7 @@ nextflow_process {
ch_vdj_reference = Channel.of( vdj_reference )
ch_cmo_fastqs_10k_pbmc_cmo = Channel.of( cmo_fastqs_10k_pbmc_cmo )
.collect()
.map { reads -> [ [ id:cmo_fastq_samplename_10k_pbmc_cmo ], reads ] }
.map { reads -> [ [ id:cmo_fastq_samplename_10k_pbmc_cmo ], reads, [:] ] }
ch_cmo_reference_10k_pbmc_cmo = Channel.of( cmo_reference_10k_pbmc_cmo )

// empty vdj reference
Expand Down Expand Up @@ -624,12 +624,12 @@ nextflow_process {
// create empty channels to fill unused cellranger multi arguments
// fastqs need a [ meta, ref ] structure
// references just need a path
ch_gex_fastqs = [ [:], [], [] ]
ch_vdj_fastqs = [ [:], [] ]
ch_ab_fastqs = [ [:], [] ]
ch_beam_fastqs = [ [:], [] ]
ch_cmo_fastqs = [ [:], [] ]
ch_crispr_fastqs = [ [:], [] ]
ch_gex_fastqs = [ [:], [], [:] ]
ch_vdj_fastqs = [ [:], [], [:] ]
ch_ab_fastqs = [ [:], [], [:] ]
ch_beam_fastqs = [ [:], [], [:] ]
ch_cmo_fastqs = [ [:], [], [:] ]
ch_crispr_fastqs = [ [:], [], [:] ]
ch_gex_frna_probeset = []
ch_gex_targetpanel = []
ch_vdj_primer_index = []
Expand All @@ -649,10 +649,10 @@ nextflow_process {
ch_vdj_reference = Channel.of( vdj_reference )
ch_bcell_fastqs_10k_pbmc = Channel.of( bcell_fastqs_10k_pbmc )
.collect()
.map { reads -> [ [ id:bcell_fastq_samplename_10k_pbmc ], reads ] }
.map { reads -> [ [ id:bcell_fastq_samplename_10k_pbmc ], reads, [:] ] }
ch_ab_fastqs_10k_pbmc = Channel.of( ab_fastqs_10k_pbmc )
.collect()
.map { reads -> [ [ id:fivepab_fastq_samplename_10k_pbmc ], reads ] }
.map { reads -> [ [ id:fivepab_fastq_samplename_10k_pbmc ], reads, [:] ] }
ch_ab_reference_10k_pbmc = Channel.of( fb_reference_10k_pbmc )

ch_gex_fastqs_5k_cmvpos_tcells = Channel.of( gex_fastqs_5k_cmvpos_tcells )
Expand All @@ -661,11 +661,11 @@ nextflow_process {
ch_vdj_reference = Channel.of( vdj_reference )
ch_vdj_fastqs_5k_cmvpos_tcells = Channel.of( vdj_fastqs_5k_cmvpos_tcells )
.collect()
.map { reads -> [ [ id:vdj_fastq_samplename_5k_cmvpos_tcells ], reads ] }
.map { reads -> [ [ id:vdj_fastq_samplename_5k_cmvpos_tcells ], reads, [:] ] }
ch_fb_reference_5k_cmvpos_tcells = Channel.of( fb_reference_5k_cmvpos_tcells )
ch_ab_fastqs_5k_cmvpos_tcells = Channel.of( ab_fastqs_5k_cmvpos_tcells )
.collect()
.map { reads -> [ [ id:ab_fastq_samplename_5k_cmvpos_tcells ], reads ] }
.map { reads -> [ [ id:ab_fastq_samplename_5k_cmvpos_tcells ], reads, [:] ] }

//
// execution
Expand Down Expand Up @@ -779,12 +779,12 @@ nextflow_process {
// create empty channels to fill unused cellranger multi arguments
// fastqs need a [ meta, ref ] structure
// references just need a path
ch_gex_fastqs = [ [:], [], [] ]
ch_vdj_fastqs = [ [:], [] ]
ch_ab_fastqs = [ [:], [] ]
ch_beam_fastqs = [ [:], [] ]
ch_cmo_fastqs = [ [:], [] ]
ch_crispr_fastqs = [ [:], [] ]
ch_gex_fastqs = [ [:], [], [:] ]
ch_vdj_fastqs = [ [:], [], [:] ]
ch_ab_fastqs = [ [:], [], [:] ]
ch_beam_fastqs = [ [:], [], [:] ]
ch_cmo_fastqs = [ [:], [], [:] ]
ch_crispr_fastqs = [ [:], [], [:] ]
ch_gex_frna_probeset = []
ch_gex_targetpanel = []
ch_vdj_reference = []
Expand All @@ -802,11 +802,11 @@ nextflow_process {

ch_gex_fastqs_sc3_v3_5k_a549 = Channel.of( test_10x_sc3_v3_5k_a549_gex )
.collect()
.map { reads -> [ [ id:test_10x_sc3_v3_5k_a549_gex_samplename ], reads, [ "expect-cells":"5000", chemistry:"SC3Pv3", "create-bam":false, "no-secondary":true ] ] }
.map { reads -> [ [ id:test_10x_sc3_v3_5k_a549_gex_samplename ], reads, [ "expect-cells":"5000", chemistry:"SC3Pv3", "create-bam":false ] ] }

ch_crispr_fastqs_sc3_v3_5k_a549 = Channel.of( test_10x_sc3_v3_5k_a549_crispr )
.collect()
.map { reads -> [ [ id:test_10x_sc3_v3_5k_a549_crispr_samplename ], reads ] }
.map { reads -> [ [ id:test_10x_sc3_v3_5k_a549_crispr_samplename ], reads, [:] ] }

ch_crispr_reference_sc3_v3_5k_a549 = Channel.of( test_10x_sc3_v3_5k_a549_crispr_fb_reference )

Expand Down Expand Up @@ -896,12 +896,12 @@ nextflow_process {
// create empty channels to fill unused cellranger multi arguments
// fastqs need a [ meta, ref ] structure
// references just need a path
ch_gex_fastqs = [ [:], [], [] ]
ch_vdj_fastqs = [ [:], [] ]
ch_ab_fastqs = [ [:], [] ]
ch_beam_fastqs = [ [:], [] ]
ch_cmo_fastqs = [ [:], [] ]
ch_crispr_fastqs = [ [:], [] ]
ch_gex_fastqs = [ [:], [], [:] ]
ch_vdj_fastqs = [ [:], [], [:] ]
ch_ab_fastqs = [ [:], [], [:] ]
ch_beam_fastqs = [ [:], [], [:] ]
ch_cmo_fastqs = [ [:], [], [:] ]
ch_crispr_fastqs = [ [:], [], [:] ]
ch_gex_frna_probeset = []
ch_gex_targetpanel = []
ch_vdj_reference = []
Expand Down