nf-core · ggabernet · Nov 26, 2024 · Nov 5, 2024 · Nov 5, 2024 · Nov 25, 2024
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
 
-## [4.2.0] - dev
+## [4.2.0] - Evanesco
 
 ### `Added`
 
@@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 - [#344](https://github.com/nf-core/airrflow/pull/344) Added option to save non-productive sequences
 - [#344](https://github.com/nf-core/airrflow/pull/344) Allow for maskprimers align with UMI on both V gene and C gene primers.
 - [#344](https://github.com/nf-core/airrflow/pull/344) Update pipeline template to nf-core tools v3.0.2.
+- [357](https://github.com/nf-core/airrflow/pull/357) Deprecate isotype_column parameter in favor of annotating C region from internal c_region alignment or c_primer alignment into the c_call column.
 
 ### `Fixed`
 
@@ -24,8 +25,15 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 ### `Dependencies`
 
+| Dependency | Old version | New version |
+| ---------- | ----------- | ----------- |
+| enchantr   | 0.1.16      | 0.1.19      |
+| presto     | 0.7.1       | 0.7.2       |
+
 ### `Deprecated parameters`
 
+- `isotype_column`: if `c_call` column value is NA, now `c_region` and `c_primer` column values respectively are annotated into the `c_call` column.
+
 ## [4.1.0] - Avenseguim
 
 ### `Added`

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -2,7 +2,7 @@ report_comment: >
 
   This report has been generated by the <a href="https://github.com/nf-core/airrflow/releases/tag/4.0" target="_blank">nf-core/airrflow</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/airrflow/4.1.0/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/airrflow/4.2.0/docs/output" target="_blank">documentation</a>.
 
 module_order:
   - fastqc:

diff --git a/assets/tutorial/airrflow.sh b/assets/tutorial/airrflow.sh
@@ -1,4 +1,4 @@
-nextflow run nf-core/airrflow -r 4.1.0 \
+nextflow run nf-core/airrflow -r 4.2.0 \
 -profile docker \
 --mode assembled \
 --input samplesheet.tsv \

diff --git a/conf/clontech_umi_bcr.config b/conf/clontech_umi_bcr.config
@@ -38,5 +38,4 @@ params {
     primer_r1_maxerror = 0.2
     assemblepairs_sequential = true
     primer_consensus = 0.6
-    isotype_column = 'cregion'
 }
diff --git a/conf/modules.config b/conf/modules.config
@@ -154,7 +154,7 @@ process {
             mode: params.publish_dir_mode,
             pattern: "*{txt,log,tab}"
         ]
-        ext.args = '--skiprc --pf CPRIMER'
+        ext.args = '--skiprc --pf C_PRIMER'
         ext.args2 = '-f ID PRIMER ERROR'
     }
 
@@ -164,7 +164,7 @@ process {
             mode: params.publish_dir_mode,
             pattern: "*{txt,log,tab}"
         ]
-        ext.args = '--skiprc --revpr --pf CREGION'
+        ext.args = '--skiprc --revpr --pf C_REGION'
         ext.args2 = '-f ID PRIMER ERROR --outname cregion_alignment'
     }
 
@@ -269,7 +269,7 @@ process {
             mode: params.publish_dir_mode,
             pattern: "*{txt,log,tab}"
         ]
-        ext.args = '--1f CREGION --coord illumina'
+        ext.args = '--1f C_REGION --coord illumina'
     }
 
     withName: PRESTO_PAIRSEQ_EXTRACT {
@@ -331,8 +331,8 @@ process {
             mode: params.publish_dir_mode,
             pattern: "*{txt,log,tab}"
         ]
-        // Use homogeneous CPRIMER for consensus
-        ext.args = ["--pf CPRIMER --maxerror ${params.buildconsensus_maxerror} --maxgap ${params.buildconsensus_maxgap}",
+        // Use homogeneous C_PRIMER for consensus
+        ext.args = ["--pf C_PRIMER --maxerror ${params.buildconsensus_maxerror} --maxgap ${params.buildconsensus_maxgap}",
             params.primer_consensus ? "--prcons $params.primer_consensus" : "",
             params.cluster_sets ? "--bf CLUSTER" : "--bf BARCODE",
             ].join(" ").trim()
@@ -416,7 +416,7 @@ process {
             enabled: false
         ]
         ext.subcommand = 'rename'
-        ext.args = '-f PRCONS -k CREGION'
+        ext.args = '-f PRCONS -k C_REGION'
     }
 
     withName: PRESTO_PARSEHEADERS_PRIMERS_SANS_UMI {
@@ -449,7 +449,7 @@ process {
             mode: params.publish_dir_mode,
             pattern: "*{txt,log,tab}"
         ]
-        ext.args = '-n 0 --inner --uf CREGION --cf CONSCOUNT --act sum --keepmiss'
+        ext.args = '-n 0 --inner --uf C_REGION --cf CONSCOUNT --act sum --keepmiss'
         ext.args2 = '-f HEADER DUPCOUNT CONSCOUNT'
     }
 
@@ -459,7 +459,7 @@ process {
             mode: params.publish_dir_mode,
             pattern: "*{txt,log,tab}"
         ]
-        ext.args = '-n 0 --inner --uf PRCONS CREGION --cf CONSCOUNT --act sum --keepmiss'
+        ext.args = '-n 0 --inner --uf PRCONS C_REGION --cf CONSCOUNT --act sum --keepmiss'
         ext.args2 = '-f HEADER DUPCOUNT CONSCOUNT'
     }
 
@@ -495,7 +495,7 @@ process {
     // V(D)J annotation
     // -----------------
 
-    withName: FETCH_DATABASES {
+    withName: 'FETCH_*' {
         publishDir = [
             path: { "${params.outdir}/databases" },
             mode: params.publish_dir_mode,

diff --git a/conf/nebnext_umi_bcr.config b/conf/nebnext_umi_bcr.config
@@ -35,5 +35,4 @@ params {
     cregion_maxlen = 100
     cregion_maxerror = 0.3
     cregion_mask_mode = 'tag'
-    isotype_column = 'cregion'
 }
diff --git a/conf/test.config b/conf/test.config
@@ -37,7 +37,6 @@ params {
     umi_start = 6
     umi_position = 'R1'
     index_file = true
-    isotype_column = 'c_primer'
     lineage_trees = true
 }
 

diff --git a/conf/test_fetchimgt.config b/conf/test_fetchimgt.config
@@ -35,7 +35,6 @@ params {
     umi_start = 6
     umi_position = 'R1'
     index_file = true
-    isotype_column = 'c_primer'
 }
 
 process{

diff --git a/conf/test_full.config b/conf/test_full.config
@@ -36,7 +36,6 @@ params {
     umi_length = 15
     umi_start = 0
     umi_position = 'R1'
-    isotype_column = 'c_primer'
 }
 
 process {

diff --git a/conf/test_maskprimers_align.config b/conf/test_maskprimers_align.config
@@ -36,6 +36,5 @@ params {
     umi_start = 6
     umi_position = 'R1'
     index_file = true
-    isotype_column = 'c_primer'
     maskprimers_align = true
 }
diff --git a/conf/test_maskprimers_extract.config b/conf/test_maskprimers_extract.config
@@ -35,7 +35,6 @@ params {
     umi_start = 6
     umi_position = 'R1'
     index_file = true
-    isotype_column = 'c_primer'
     lineage_trees = false
     primer_r1_mask_mode = 'trim'
     primer_r2_mask_mode = 'cut'

diff --git a/conf/test_no_umi.config b/conf/test_no_umi.config
@@ -26,7 +26,6 @@ params {
     vprimer_start = 4
     primer_revpr = true
     umi_length = 0
-    isotype_column = 'c_primer'
 
     // Input data
     input = pipelines_testdata_base_path + 'testdata-no-umi/Metadata_test-no-umi_airr.tsv'

diff --git a/conf/test_nocluster.config b/conf/test_nocluster.config
@@ -38,7 +38,6 @@ params {
     cluster_sets = false
     index_file = true
     clonal_threshold = 0.15
-    isotype_column = 'c_primer'
 }
 
 process{

diff --git a/conf/test_raw_immcantation_devel.config b/conf/test_raw_immcantation_devel.config
@@ -37,7 +37,6 @@ params {
     umi_start = 6
     umi_position = 'R1'
     index_file = true
-    isotype_column = 'c_primer'
 }
 
 process{

diff --git a/modules/local/airrflow_report/airrflow_report.nf b/modules/local/airrflow_report/airrflow_report.nf
@@ -5,7 +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 "docker.io/immcantation/airrflow:4.1.0"
+    container "docker.io/immcantation/airrflow:4.2.0"
 
     input:
     tuple val(meta), path(tab) // sequence tsv table in AIRR format

diff --git a/modules/local/enchantr/collapse_duplicates.nf b/modules/local/enchantr/collapse_duplicates.nf
@@ -7,7 +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 "docker.io/immcantation/airrflow:4.1.0"
+    container "docker.io/immcantation/airrflow:4.2.0"
 
     input:
     tuple val(meta), path(tabs) // tuple [val(meta), sequence tsv in AIRR format ]

diff --git a/modules/local/enchantr/define_clones.nf b/modules/local/enchantr/define_clones.nf
@@ -24,7 +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 "docker.io/immcantation/airrflow:4.1.0"
+    container "docker.io/immcantation/airrflow:4.2.0"
 
     input:
     tuple val(meta), path(tabs) // meta, sequence tsv in AIRR format
@@ -59,7 +59,6 @@ process DEFINE_CLONES {
                                         'threshold'=${thr}, \\
                                         'singlecell'='${params.singlecell}', \\
                                         'outdir'=getwd(), \\
-                                        'isotype_column'='${params.isotype_column}', \\
                                         'nproc'=${task.cpus}, \\
                                         'log'='${meta.id}_clone_command_log' ${args}))"
 

diff --git a/modules/local/enchantr/detect_contamination.nf b/modules/local/enchantr/detect_contamination.nf
@@ -8,7 +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 "docker.io/immcantation/airrflow:4.1.0"
+    container "docker.io/immcantation/airrflow:4.2.0"
 
     input:
     path(tabs)

diff --git a/modules/local/enchantr/dowser_lineages.nf b/modules/local/enchantr/dowser_lineages.nf
@@ -24,7 +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 "docker.io/immcantation/airrflow:4.1.0"
+    container "docker.io/immcantation/airrflow:4.2.0"
 
     input:
     tuple val(meta), path(tabs)

diff --git a/modules/local/enchantr/find_threshold.nf b/modules/local/enchantr/find_threshold.nf
@@ -24,7 +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 "docker.io/immcantation/airrflow:4.1.0"
+    container "docker.io/immcantation/airrflow:4.2.0"
 
 
     input:

diff --git a/modules/local/enchantr/remove_chimeric.nf b/modules/local/enchantr/remove_chimeric.nf
@@ -8,7 +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 "docker.io/immcantation/airrflow:4.1.0"
+    container "docker.io/immcantation/airrflow:4.2.0"
 
 
     input:

diff --git a/modules/local/enchantr/report_file_size.nf b/modules/local/enchantr/report_file_size.nf
@@ -9,7 +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 "docker.io/immcantation/airrflow:4.1.0"
+    container "docker.io/immcantation/airrflow:4.2.0"
 
     input:
     path logs

diff --git a/modules/local/enchantr/single_cell_qc.nf b/modules/local/enchantr/single_cell_qc.nf
@@ -23,7 +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 "docker.io/immcantation/airrflow:4.1.0"
+    container "docker.io/immcantation/airrflow:4.2.0"
 
     input:
     path(tabs)

diff --git a/modules/local/enchantr/validate_input.nf b/modules/local/enchantr/validate_input.nf
@@ -9,7 +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 "docker.io/immcantation/airrflow:4.1.0"
+    container "docker.io/immcantation/airrflow:4.2.0"
 
     input:
     file samplesheet

diff --git a/modules/local/reveal/add_meta_to_tab.nf b/modules/local/reveal/add_meta_to_tab.nf
@@ -6,7 +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 "docker.io/immcantation/airrflow:4.1.0"
+    container "docker.io/immcantation/airrflow:4.2.0"
 
     cache 'deep' // Without 'deep' this process would run when using -resume
 

diff --git a/modules/local/reveal/filter_junction_mod3.nf b/modules/local/reveal/filter_junction_mod3.nf
@@ -6,7 +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 "docker.io/immcantation/airrflow:4.1.0"
+    container "docker.io/immcantation/airrflow:4.2.0"
 
     input:
     tuple val(meta), path(tab) // sequence tsv in AIRR format

diff --git a/modules/local/reveal/filter_quality.nf b/modules/local/reveal/filter_quality.nf
@@ -6,7 +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 "docker.io/immcantation/airrflow:4.1.0"
+    container "docker.io/immcantation/airrflow:4.2.0"
 
     input:
     tuple val(meta), path(tab) // sequence tsv in AIRR format

diff --git a/nextflow.config b/nextflow.config
@@ -88,7 +88,6 @@ params {
     reference_fasta = "${params.pipelines_testdata_base_path}database-cache/imgtdb_base.zip"
     fetch_imgt = false
     save_databases = true
-    isotype_column = 'c_call'
     skip_alignment_filter = false
 
     // -----------------------
@@ -375,7 +374,7 @@ manifest {
     description     = """B and T cell repertoire analysis pipeline with the Immcantation framework."""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=24.04.2'
-    version         = '4.1.0'
+    version         = '4.2.0'
     doi             = 'https://doi.org/10.1371/journal.pcbi.1012265'
 }
 

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -395,13 +395,6 @@
                     "type": "boolean",
                     "description": "Set this flag to fetch the IMGT reference data at runtime.",
                     "fa_icon": "fas fa-cloud-download-alt"
-                },
-                "isotype_column": {
-                    "type": "string",
-                    "description": "Set the column in the AIRR rearrangement file that isotype information should be gathered from.",
-                    "default": "c_call",
-                    "fa_icon": "fas fa-border-all",
-                    "help_text": "Default is the `c_call` column. For bulk protocols one can use the c_primers or cregion columns (check `align_cregion`). The primer or cregions fasta file header need to contain the strings `IGHA`, `IGHD`, `IGHG`... for the isotypes to be properly parsed. This will be used for plotting mutation frequency by isotype in the clonal analysis report."
                 }
             },
             "fa_icon": "fas fa-edit"

diff --git a/subworkflows/local/presto_umi.nf b/subworkflows/local/presto_umi.nf
@@ -435,7 +435,7 @@ workflow PRESTO_UMI {
 
     // Build consensus of sequences with same UMI barcode
     if (params.maskprimers_align_race) {
-        // Only consider CPRIMER frequency when building consensus
+        // Only consider C_PRIMER frequency when building consensus
         PRESTO_BUILDCONSENSUS_ALIGN_RACE (
             ch_for_buildconsensus
         )