Fix nextflow lint warnings: deprecated Channel factories, implicit closures,

unused params, single-emit names, and projectDir-in-process

Replaces deprecated `Channel.*` factory calls with lowercase `channel.*`
across 9 files, declares explicit closure parameters in place of implicit
`it` (sc_to_bulk.nf, singlecell.nf), and prefixes unused branch/map closure
parameters with `_` in pseudobulk_qc.nf.

Removes the emit name on three subworkflows with a single output
(COMPARE.shared_cdr3, CONVERT.sample_map_converted, REPORT.rendered_html)
and updates every call site accordingly (bulktcr_analysis.nf, tcrtoolkit.nf).
CONVERT's conditional assignment is restructured using the ternary-in-emit
idiom already established in patient.nf, since its emit couldn't just drop
a name while remaining a plain if/else-assigned variable.

Fixes cluster_to_sc.nf's discouraged `${projectDir}/bin/...` reference by
invoking enrich_seurat.R by bare name instead - it already carries the same
shebang and executable bit as every Python script in bin/, so Nextflow's
automatic bin/-on-PATH staging resolves it exactly like the rest of the
pipeline's scripts, without adding a new process input.

Also drops an unused `def sample_stats_agg =` binding in sample.nf, keeping
the collectFile/storeDir call for its file-publishing side effect.

Warnings: 48 -> 4 (remaining 4 are linter false positives: sample_map/
concat_cdr3 are read via bare `emit:` references, which the linter's
"declared but not used" check doesn't detect as usage).

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

Author: dltamayo

modules/bridges/cluster_to_sc.nf

@@ -41,7 +41,7 @@ process CLUSTER_TO_SC {
 
     script:
     """
-    Rscript ${projectDir}/bin/enrich_seurat.R \\
+    enrich_seurat.R \\
         --seurat_rds     "${seurat_rds}" \\
         --export_cells   "${export_cells}" \\
         --tcrdist_radius ${tcrdist_radius}

subworkflows/bridges/sc_to_bulk.nf

@@ -23,7 +23,7 @@ workflow SC_TO_BULK_SW {
         params.condition_col,
         params.timepoint_col,
         params.batch_col
-    ].findAll { it }.join(',')
+    ].findAll { col -> col }.join(',')
 
     // TCELL_INTEGRATION always exports a standardized 'sample' column;
     // params.sample_col is the Seurat metadata name, not the export column name.

subworkflows/local/bulktcr_analysis.nf

@@ -86,7 +86,7 @@ workflow BULKTCR_ANALYSIS {
 
         ch_discovery_report = sample_stats_agg
             .combine(ANNOTATE.out.concat_cdr3_sorted)
-            .combine(COMPARE.out.shared_cdr3)
+            .combine(COMPARE.out)
             .combine(SAMPLE.out.tcrdist_files.map { l -> [l] })
             .combine(SAMPLE.out.vdjdb_files.map { l -> [l] })
             .combine(convert_files.map { l -> [l] })
@@ -144,7 +144,7 @@ workflow BULKTCR_ANALYSIS {
 
         def details_part2_base = sample_stats_agg
             .combine(ANNOTATE.out.concat_cdr3_sorted)
-            .combine(COMPARE.out.shared_cdr3)
+            .combine(COMPARE.out)
 
         def run_patient_clustering = levels.contains('patient')
         def patient_clustering_notebook = run_patient_clustering
@@ -238,5 +238,5 @@ workflow BULKTCR_ANALYSIS {
     gliph2_cluster_member_details  = levels.contains('patient') ? PATIENT.out.gliph2_cluster_member_details  : channel.value([])
     gliph2_global_similarities     = levels.contains('patient') ? PATIENT.out.gliph2_global_similarities     : channel.value([])
 
-    shared_cdr3 = levels.contains('compare') ? COMPARE.out.shared_cdr3 : channel.empty()
+    shared_cdr3 = levels.contains('compare') ? COMPARE.out : channel.empty()
 }

subworkflows/local/compare.nf

@@ -35,5 +35,5 @@ workflow COMPARE {
     )
 
     emit:
-        shared_cdr3 = TCRSHARING_CALC.out.shared_cdr3
+        TCRSHARING_CALC.out.shared_cdr3
 }

subworkflows/local/convert.nf

@@ -25,11 +25,8 @@ workflow CONVERT {
             file(params.airr_schema),
             file(params.imgt_lookup)
         )
-        sample_map_converted = CONVERT_ADAPTIVE.out.adaptive_convert
-    } else {
-        sample_map_converted = sample_map
     }
 
     emit:
-    sample_map_converted
+    input_format == 'adaptive' ? CONVERT_ADAPTIVE.out.adaptive_convert : sample_map
 }

subworkflows/local/pseudobulk_qc.nf

@@ -39,22 +39,22 @@ workflow PSEUDOBULK_QC_SW {
 
     // Wrap the scalar thresholds as explicit value channels. Nextflow 24.10 does not
     // reliably auto-broadcast a bare value passed alongside a queue-channel input.
-    PSEUDOBULK_QC_CALC( sample_map, Channel.value(min_clones), Channel.value(min_cells) )
+    PSEUDOBULK_QC_CALC( sample_map, channel.value(min_clones), channel.value(min_cells) )
 
-    branched = PSEUDOBULK_QC_CALC.out.scored.branch { meta, file, qc_pass, nc, ce ->
+    branched = PSEUDOBULK_QC_CALC.out.scored.branch { _meta, _file, qc_pass, _nc, _ce ->
         pass: qc_pass == 'PASS'
         fail: true
     }
 
     // Log every dropped sample
-    branched.fail.view { meta, file, qc_pass, nc, ce ->
+    branched.fail.view { meta, _file, _qc_pass, nc, ce ->
         "[Pseudobulk QC] DROPPED '${meta.sample}': clones=${nc} (min ${min_clones}), cells=${ce} (min ${min_cells})"
     }
 
     // Optional hard-stop: abort the run if any sample fails QC
     if (gate_mode == 'hard_stop') {
         branched.fail
-            .map { meta, file, qc_pass, nc, ce -> "${meta.sample} (clones=${nc}, cells=${ce})" }
+            .map { meta, _file, _qc_pass, nc, ce -> "${meta.sample} (clones=${nc}, cells=${ce})" }
             .collect()
             .subscribe { failed ->
                 if (failed) {
@@ -66,7 +66,7 @@ workflow PSEUDOBULK_QC_SW {
     }
 
     // Passing samples only -> [meta, file]
-    passed_map = branched.pass.map { meta, file, qc_pass, nc, ce -> [meta, file] }
+    passed_map = branched.pass.map { meta, file, _qc_pass, _nc, _ce -> [meta, file] }
 
     // Warn (drop mode) if nothing survived the gate
     passed_map.count().subscribe { n ->
@@ -78,7 +78,7 @@ workflow PSEUDOBULK_QC_SW {
 
     // Rebuild concatenated CDR3 from passing samples (for ANNOTATE)
     concat_cdr3 = passed_map
-        .map { meta, file -> file }
+        .map { _meta, file -> file }
         .collectFile(name: 'concat_cdr3.tsv', keepHeader: true, skip: 1)
 
     // ── Reporting (non-redundant): QC summary + V gene-family usage ──────────

subworkflows/local/report.nf

@@ -27,5 +27,5 @@ workflow REPORT {
     )
 
     emit:
-        rendered_html = RENDER_NOTEBOOK.out
+        RENDER_NOTEBOOK.out
 }

subworkflows/local/sample.nf

@@ -33,7 +33,9 @@ workflow SAMPLE {
     def sample_calc_input = processed_samples.join(per_sample_stats)
     SAMPLE_CALC( sample_calc_input )
 
-    def sample_stats_agg = SAMPLE_CALC.out.sample_csv
+    // Published as a side effect (storeDir) - the aggregated CSV itself isn't consumed
+    // further downstream; bulktcr_analysis.nf computes its own in-memory copy for reports.
+    SAMPLE_CALC.out.sample_csv
         .collectFile(name: "sample_stats.csv", keepHeader: true, skip: 1, sort: true, storeDir: "${params.outdir}/sample")
 
     def v_family_agg = SAMPLE_CALC.out.v_family_csv

subworkflows/scratch/conga.nf

@@ -10,7 +10,7 @@ workflow CONGA_SW {
     project_name
 
     main:
-    ch_notebook = Channel.fromPath(
+    ch_notebook = channel.fromPath(
         "${projectDir}/modules/scratch/CONGA/CoNGA_Report.qmd",
         checkIfExists: true
     )

subworkflows/scratch/consensus_clustering.nf

@@ -13,7 +13,7 @@ workflow CONSENSUS_SW {
     project_name
 
     main:
-    ch_notebook = Channel.fromPath(
+    ch_notebook = channel.fromPath(
         "${projectDir}/modules/scratch/CONSENSUS_CLUSTERING/Clonotype_Clustering_Consensus_Report.qmd",
         checkIfExists: true
     )