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Apply PR review comments #338

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merged 3 commits into from
May 31, 2024
Merged

Apply PR review comments #338

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39d5270
add tutorial
ggabernet May 31, 2024
efda2c4
simplify container
ggabernet May 31, 2024
0d30d4c
update test data param
ggabernet May 31, 2024
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8 changes: 8 additions & 0 deletions assets/tutorial/airrflow.sh
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@@ -0,0 +1,8 @@
nextflow run nf-core/airrflow -r 4.1.0 \
-profile docker \
--mode assembled \
--input samplesheet.tsv \
--outdir results \
-w work \
--max_cpus 12 \
--max_memory 12.GB
6 changes: 6 additions & 0 deletions assets/tutorial/samplesheet.tsv
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filename species subject_id sample_id day tissue sex age biomaterial_provider pcr_target_locus single_cell
https://zenodo.org/records/11373741/files/AIRR_subject1_FNA_d0_1_Y1.tsv human S1 S1_d0 d0 PMBC NA NA NA IG TRUE
https://zenodo.org/records/11373741/files/AIRR_subject1_FNA_d12_3_Y1.tsv human S1 S1_d12 d12 PMBC NA NA NA IG TRUE
https://zenodo.org/records/11373741/files/AIRR_subject2_FNA_d0_1_Y1.tsv human S2 S2_d0 d0 PMBC NA NA NA IG TRUE
https://zenodo.org/records/11373741/files/AIRR_subject2_FNA_d12_2_Y1.tsv human S2 S2_d12 d12 PMBC NA NA NA IG TRUE

10 changes: 5 additions & 5 deletions conf/test.config
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Expand Up @@ -20,11 +20,11 @@ params {
max_time = '6.h'

// Input data
input = pipelines_testdata_base_path + 'airrflow/testdata-bcr/Metadata_test_airr.tsv'
cprimers = pipelines_testdata_base_path + 'airrflow/testdata-bcr/C_primers.fasta'
vprimers = pipelines_testdata_base_path + 'airrflow/testdata-bcr/V_primers.fasta'
reference_fasta = pipelines_testdata_base_path + 'airrflow/database-cache/imgtdb_base.zip'
reference_igblast = pipelines_testdata_base_path + 'airrflow/database-cache/igblast_base.zip'
input = pipelines_testdata_base_path + 'testdata-bcr/Metadata_test_airr.tsv'
cprimers = pipelines_testdata_base_path + 'testdata-bcr/C_primers.fasta'
vprimers = pipelines_testdata_base_path + 'testdata-bcr/V_primers.fasta'
reference_fasta = pipelines_testdata_base_path + 'database-cache/imgtdb_base.zip'
reference_igblast = pipelines_testdata_base_path + 'database-cache/igblast_base.zip'

mode = 'fastq'

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4 changes: 2 additions & 2 deletions conf/test_10x_sc.config
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Expand Up @@ -23,6 +23,6 @@ params {


// Input data
input = pipelines_testdata_base_path + 'airrflow/testdata-sc/10x_sc_raw.tsv'
reference_10x = pipelines_testdata_base_path + 'airrflow/testdata-sc/refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0.tar.gz'
input = pipelines_testdata_base_path + 'testdata-sc/10x_sc_raw.tsv'
reference_10x = pipelines_testdata_base_path + 'testdata-sc/refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0.tar.gz'
}
6 changes: 3 additions & 3 deletions conf/test_assembled_hs.config
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Expand Up @@ -18,9 +18,9 @@ params {

// Input data
mode = 'assembled'
input = pipelines_testdata_base_path + 'airrflow/testdata-reveal/test_assembled_metadata_hs.tsv'
reference_fasta = pipelines_testdata_base_path + 'airrflow/database-cache/imgtdb_base.zip'
reference_igblast = pipelines_testdata_base_path + 'airrflow/database-cache/igblast_base.zip'
input = pipelines_testdata_base_path + 'testdata-reveal/test_assembled_metadata_hs.tsv'
reference_fasta = pipelines_testdata_base_path + 'database-cache/imgtdb_base.zip'
reference_igblast = pipelines_testdata_base_path + 'database-cache/igblast_base.zip'

reassign = true
productive_only = true
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6 changes: 3 additions & 3 deletions conf/test_assembled_immcantation_devel_hs.config
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Expand Up @@ -18,9 +18,9 @@ params {

// Input data
mode = 'assembled'
input = pipelines_testdata_base_path + 'airrflow/testdata-reveal/test_assembled_metadata_hs.tsv'
reference_fasta = pipelines_testdata_base_path + 'airrflow/database-cache/imgtdb_base.zip'
reference_igblast = pipelines_testdata_base_path + 'airrflow/database-cache/igblast_base.zip'
input = pipelines_testdata_base_path + 'testdata-reveal/test_assembled_metadata_hs.tsv'
reference_fasta = pipelines_testdata_base_path + 'database-cache/imgtdb_base.zip'
reference_igblast = pipelines_testdata_base_path + 'database-cache/igblast_base.zip'

reassign = true
productive_only = true
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6 changes: 3 additions & 3 deletions conf/test_assembled_immcantation_devel_mm.config
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Expand Up @@ -18,9 +18,9 @@ params {

// Input data
mode = 'assembled'
input = pipelines_testdata_base_path + 'airrflow/testdata-reveal/test_assembled_metadata_mm.tsv'
reference_fasta = pipelines_testdata_base_path + 'airrflow/database-cache/imgtdb_base.zip'
reference_igblast = pipelines_testdata_base_path + 'airrflow/database-cache/igblast_base.zip'
input = pipelines_testdata_base_path + 'testdata-reveal/test_assembled_metadata_mm.tsv'
reference_fasta = pipelines_testdata_base_path + 'database-cache/imgtdb_base.zip'
reference_igblast = pipelines_testdata_base_path + 'database-cache/igblast_base.zip'

reassign = true
productive_only = true
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6 changes: 3 additions & 3 deletions conf/test_assembled_mm.config
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Expand Up @@ -18,9 +18,9 @@ params {

// Input data
mode = 'assembled'
input = pipelines_testdata_base_path + 'airrflow/testdata-reveal/test_assembled_metadata_mm.tsv'
reference_fasta = pipelines_testdata_base_path + 'airrflow/database-cache/imgtdb_base.zip'
reference_igblast = pipelines_testdata_base_path + 'airrflow/database-cache/igblast_base.zip'
input = pipelines_testdata_base_path + 'testdata-reveal/test_assembled_metadata_mm.tsv'
reference_fasta = pipelines_testdata_base_path + 'database-cache/imgtdb_base.zip'
reference_igblast = pipelines_testdata_base_path + 'database-cache/igblast_base.zip'

reassign = true
productive_only = true
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6 changes: 3 additions & 3 deletions conf/test_clontech_umi.config
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Expand Up @@ -21,10 +21,10 @@ params {
max_time = '6.h'

// Input data
input = pipelines_testdata_base_path +'airrflow/testdata-clontech/samplesheet.tsv'
input = pipelines_testdata_base_path +'testdata-clontech/samplesheet.tsv'

reference_fasta = pipelines_testdata_base_path + 'airrflow/database-cache/imgtdb_base.zip'
reference_igblast = pipelines_testdata_base_path + 'airrflow/database-cache/igblast_base.zip'
reference_fasta = pipelines_testdata_base_path + 'database-cache/imgtdb_base.zip'
reference_igblast = pipelines_testdata_base_path + 'database-cache/igblast_base.zip'

clonal_threshold = 0.1

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6 changes: 3 additions & 3 deletions conf/test_fetchimgt.config
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Expand Up @@ -20,9 +20,9 @@ params {
max_time = '6.h'

// Input data
input = pipelines_testdata_base_path + 'airrflow/testdata-bcr/Metadata_test_airr.tsv'
cprimers = pipelines_testdata_base_path + 'airrflow/testdata-bcr/C_primers.fasta'
vprimers = pipelines_testdata_base_path + 'airrflow/testdata-bcr/V_primers.fasta'
input = pipelines_testdata_base_path + 'testdata-bcr/Metadata_test_airr.tsv'
cprimers = pipelines_testdata_base_path + 'testdata-bcr/C_primers.fasta'
vprimers = pipelines_testdata_base_path + 'testdata-bcr/V_primers.fasta'
fetch_imgt = true

mode = 'fastq'
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6 changes: 3 additions & 3 deletions conf/test_full.config
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Expand Up @@ -15,11 +15,11 @@ params {
config_profile_description = 'Full test dataset to check pipeline function'

// Input data
input = pipelines_testdata_base_path + 'airrflow/testdata-bcr/metadata_pcr_umi_airr_300.tsv'
input = pipelines_testdata_base_path + 'testdata-bcr/metadata_pcr_umi_airr_300.tsv'
cprimers = 's3://ngi-igenomes/test-data/airrflow/pcr_umi/cprimers.fasta'
vprimers = 's3://ngi-igenomes/test-data/airrflow/pcr_umi/vprimers.fasta'
reference_fasta = pipelines_testdata_base_path + 'airrflow/database-cache/imgtdb_base.zip'
reference_igblast = pipelines_testdata_base_path + 'airrflow/database-cache/igblast_base.zip'
reference_fasta = pipelines_testdata_base_path + 'database-cache/imgtdb_base.zip'
reference_igblast = pipelines_testdata_base_path + 'database-cache/igblast_base.zip'

lineage_trees = true

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6 changes: 3 additions & 3 deletions conf/test_nebnext_umi.config
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Expand Up @@ -22,10 +22,10 @@ params {
max_time = '6.h'

// Input data
input = pipelines_testdata_base_path + 'airrflow/testdata-neb/samplesheet.tsv'
input = pipelines_testdata_base_path + 'testdata-neb/samplesheet.tsv'

reference_fasta = pipelines_testdata_base_path + 'airrflow/database-cache/imgtdb_base.zip'
reference_igblast = pipelines_testdata_base_path + 'airrflow/database-cache/igblast_base.zip'
reference_fasta = pipelines_testdata_base_path + 'database-cache/imgtdb_base.zip'
reference_igblast = pipelines_testdata_base_path + 'database-cache/igblast_base.zip'

clonal_threshold = 0.1

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10 changes: 5 additions & 5 deletions conf/test_no_umi.config
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Expand Up @@ -27,11 +27,11 @@ params {
isotype_column = 'c_primer'

// Input data
input = pipelines_testdata_base_path + 'airrflow/testdata-no-umi/Metadata_test-no-umi_airr.tsv'
cprimers = pipelines_testdata_base_path + 'airrflow/testdata-no-umi/Greiff2014_CPrimers.fasta'
vprimers = pipelines_testdata_base_path + 'airrflow/testdata-no-umi/Greiff2014_VPrimers.fasta'
reference_fasta = pipelines_testdata_base_path + 'airrflow/database-cache/imgtdb_base.zip'
reference_igblast = pipelines_testdata_base_path + 'airrflow/database-cache/igblast_base.zip'
input = pipelines_testdata_base_path + 'testdata-no-umi/Metadata_test-no-umi_airr.tsv'
cprimers = pipelines_testdata_base_path + 'testdata-no-umi/Greiff2014_CPrimers.fasta'
vprimers = pipelines_testdata_base_path + 'testdata-no-umi/Greiff2014_VPrimers.fasta'
reference_fasta = pipelines_testdata_base_path + 'database-cache/imgtdb_base.zip'
reference_igblast = pipelines_testdata_base_path + 'database-cache/igblast_base.zip'


}
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10 changes: 5 additions & 5 deletions conf/test_nocluster.config
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Expand Up @@ -20,11 +20,11 @@ params {
max_time = '6.h'

// Input data
input = pipelines_testdata_base_path + 'airrflow/testdata-bcr/Metadata_test_airr.tsv'
cprimers = pipelines_testdata_base_path + 'airrflow/testdata-bcr/C_primers.fasta'
vprimers = pipelines_testdata_base_path + 'airrflow/testdata-bcr/V_primers.fasta'
reference_fasta = pipelines_testdata_base_path + 'airrflow/database-cache/imgtdb_base.zip'
reference_igblast = pipelines_testdata_base_path + 'airrflow/database-cache/igblast_base.zip'
input = pipelines_testdata_base_path + 'testdata-bcr/Metadata_test_airr.tsv'
cprimers = pipelines_testdata_base_path + 'testdata-bcr/C_primers.fasta'
vprimers = pipelines_testdata_base_path + 'testdata-bcr/V_primers.fasta'
reference_fasta = pipelines_testdata_base_path + 'database-cache/imgtdb_base.zip'
reference_igblast = pipelines_testdata_base_path + 'database-cache/igblast_base.zip'

mode = 'fastq'

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10 changes: 5 additions & 5 deletions conf/test_raw_immcantation_devel.config
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Expand Up @@ -20,12 +20,12 @@ params {
max_time = '6.h'

// Input data
input = pipelines_testdata_base_path + 'airrflow/testdata-bcr/Metadata_test_airr.tsv'
cprimers = pipelines_testdata_base_path + 'airrflow/testdata-bcr/C_primers.fasta'
vprimers = pipelines_testdata_base_path + 'airrflow/testdata-bcr/V_primers.fasta'
input = pipelines_testdata_base_path + 'testdata-bcr/Metadata_test_airr.tsv'
cprimers = pipelines_testdata_base_path + 'testdata-bcr/C_primers.fasta'
vprimers = pipelines_testdata_base_path + 'testdata-bcr/V_primers.fasta'

reference_fasta = pipelines_testdata_base_path + 'airrflow/database-cache/imgtdb_base.zip'
reference_igblast = pipelines_testdata_base_path + 'airrflow/database-cache/igblast_base.zip'
reference_fasta = pipelines_testdata_base_path + 'database-cache/imgtdb_base.zip'
reference_igblast = pipelines_testdata_base_path + 'database-cache/igblast_base.zip'

mode = 'fastq'

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10 changes: 5 additions & 5 deletions conf/test_tcr.config
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Expand Up @@ -28,11 +28,11 @@ params {


// Input data
input = pipelines_testdata_base_path + 'airrflow/testdata-tcr/TCR_metadata_airr.tsv'
cprimers = pipelines_testdata_base_path + 'airrflow/testdata-tcr/cprimers.fasta'
race_linker = pipelines_testdata_base_path + 'airrflow/testdata-tcr/linker.fasta'
reference_fasta = pipelines_testdata_base_path + 'airrflow/database-cache/imgtdb_base.zip'
reference_igblast = pipelines_testdata_base_path + 'airrflow/database-cache/igblast_base.zip'
input = pipelines_testdata_base_path + 'testdata-tcr/TCR_metadata_airr.tsv'
cprimers = pipelines_testdata_base_path + 'testdata-tcr/cprimers.fasta'
race_linker = pipelines_testdata_base_path + 'testdata-tcr/linker.fasta'
reference_fasta = pipelines_testdata_base_path + 'database-cache/imgtdb_base.zip'
reference_igblast = pipelines_testdata_base_path + 'database-cache/igblast_base.zip'

}

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4 changes: 1 addition & 3 deletions modules/local/airrflow_report/airrflow_report.nf
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Expand Up @@ -5,9 +5,7 @@ process AIRRFLOW_REPORT {
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
error "nf-core/airrflow currently does not support Conda. Please use a container profile instead."
}
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'docker.io/immcantation/airrflow:4.1.0':
'docker.io/immcantation/airrflow:4.1.0' }"
container "docker.io/immcantation/airrflow:4.1.0"

input:
tuple val(meta), path(tab) // sequence tsv table in AIRR format
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4 changes: 1 addition & 3 deletions modules/local/enchantr/collapse_duplicates.nf
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Expand Up @@ -7,9 +7,7 @@ process COLLAPSE_DUPLICATES {
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
error "nf-core/airrflow currently does not support Conda. Please use a container profile instead."
}
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'docker.io/immcantation/airrflow:4.1.0':
'docker.io/immcantation/airrflow:4.1.0' }"
container "docker.io/immcantation/airrflow:4.1.0"

input:
tuple val(meta), path(tabs) // tuple [val(meta), sequence tsv in AIRR format ]
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4 changes: 1 addition & 3 deletions modules/local/enchantr/define_clones.nf
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Expand Up @@ -24,9 +24,7 @@ process DEFINE_CLONES {
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
error "nf-core/airrflow currently does not support Conda. Please use a container profile instead."
}
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'docker.io/immcantation/airrflow:4.1.0':
'docker.io/immcantation/airrflow:4.1.0' }"
container "docker.io/immcantation/airrflow:4.1.0"

input:
tuple val(meta), path(tabs) // meta, sequence tsv in AIRR format
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4 changes: 1 addition & 3 deletions modules/local/enchantr/detect_contamination.nf
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Expand Up @@ -8,9 +8,7 @@ process DETECT_CONTAMINATION {
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
error "nf-core/airrflow currently does not support Conda. Please use a container profile instead."
}
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'docker.io/immcantation/airrflow:4.1.0':
'docker.io/immcantation/airrflow:4.1.0' }"
container "docker.io/immcantation/airrflow:4.1.0"

input:
path(tabs)
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4 changes: 1 addition & 3 deletions modules/local/enchantr/dowser_lineages.nf
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Expand Up @@ -24,9 +24,7 @@ process DOWSER_LINEAGES {
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
error "nf-core/airrflow currently does not support Conda. Please use a container profile instead."
}
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'docker.io/immcantation/airrflow:4.1.0':
'docker.io/immcantation/airrflow:4.1.0' }"
container "docker.io/immcantation/airrflow:4.1.0"

input:
tuple val(meta), path(tabs)
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4 changes: 1 addition & 3 deletions modules/local/enchantr/find_threshold.nf
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Expand Up @@ -24,9 +24,7 @@ process FIND_THRESHOLD {
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
error "nf-core/airrflow currently does not support Conda. Please use a container profile instead."
}
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'docker.io/immcantation/airrflow:4.1.0':
'docker.io/immcantation/airrflow:4.1.0' }"
container "docker.io/immcantation/airrflow:4.1.0"


input:
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4 changes: 1 addition & 3 deletions modules/local/enchantr/remove_chimeric.nf
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Expand Up @@ -8,9 +8,7 @@ process REMOVE_CHIMERIC {
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
error "nf-core/airrflow currently does not support Conda. Please use a container profile instead."
}
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'docker.io/immcantation/airrflow:4.1.0':
'docker.io/immcantation/airrflow:4.1.0' }"
container "docker.io/immcantation/airrflow:4.1.0"


input:
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4 changes: 1 addition & 3 deletions modules/local/enchantr/report_file_size.nf
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Expand Up @@ -9,9 +9,7 @@ process REPORT_FILE_SIZE {
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
error "nf-core/airrflow currently does not support Conda. Please use a container profile instead."
}
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'docker.io/immcantation/airrflow:4.1.0':
'docker.io/immcantation/airrflow:4.1.0' }"
container "docker.io/immcantation/airrflow:4.1.0"

input:
path logs
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4 changes: 1 addition & 3 deletions modules/local/enchantr/single_cell_qc.nf
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Expand Up @@ -23,9 +23,7 @@ process SINGLE_CELL_QC {
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
error "nf-core/airrflow currently does not support Conda. Please use a container profile instead."
}
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'docker.io/immcantation/airrflow:4.1.0':
'docker.io/immcantation/airrflow:4.1.0' }"
container "docker.io/immcantation/airrflow:4.1.0"

input:
path(tabs)
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4 changes: 1 addition & 3 deletions modules/local/enchantr/validate_input.nf
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Expand Up @@ -9,9 +9,7 @@ process VALIDATE_INPUT {
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
error "nf-core/airrflow currently does not support Conda. Please use a container profile instead."
}
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'docker.io/immcantation/airrflow:4.1.0':
'docker.io/immcantation/airrflow:4.1.0' }"
container "docker.io/immcantation/airrflow:4.1.0"

input:
file samplesheet
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4 changes: 1 addition & 3 deletions modules/local/reveal/add_meta_to_tab.nf
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Expand Up @@ -6,9 +6,7 @@ process ADD_META_TO_TAB {
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
error "nf-core/airrflow currently does not support Conda. Please use a container profile instead."
}
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'docker.io/immcantation/airrflow:4.1.0':
'docker.io/immcantation/airrflow:4.1.0' }"
container "docker.io/immcantation/airrflow:4.1.0"

cache 'deep' // Without 'deep' this process would run when using -resume

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4 changes: 1 addition & 3 deletions modules/local/reveal/filter_junction_mod3.nf
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Expand Up @@ -6,9 +6,7 @@ process FILTER_JUNCTION_MOD3 {
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
error "nf-core/airrflow currently does not support Conda. Please use a container profile instead."
}
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'docker.io/immcantation/airrflow:4.1.0':
'docker.io/immcantation/airrflow:4.1.0' }"
container "docker.io/immcantation/airrflow:4.1.0"

input:
tuple val(meta), path(tab) // sequence tsv in AIRR format
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4 changes: 1 addition & 3 deletions modules/local/reveal/filter_quality.nf
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Expand Up @@ -6,9 +6,7 @@ process FILTER_QUALITY {
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
error "nf-core/airrflow currently does not support Conda. Please use a container profile instead."
}
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'docker.io/immcantation/airrflow:4.1.0':
'docker.io/immcantation/airrflow:4.1.0' }"
container "docker.io/immcantation/airrflow:4.1.0"

input:
tuple val(meta), path(tab) // sequence tsv in AIRR format
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2 changes: 1 addition & 1 deletion nextflow.config
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Expand Up @@ -14,7 +14,7 @@ params {
mode = "fastq"
miairr="$projectDir/assets/reveal/mapping_MiAIRR_BioSample_v1.3.1.tsv"
index_file = false
pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/'

// ----------------------------
// sequencing protocol options
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