Remove defunct parameter, update parameter comments

uclahs-cds · Jul 15, 2024 · cf0a904 · cf0a904
1 parent 9ef1a69
commit cf0a904
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Showing 2 changed files with 63 additions and 37 deletions.
diff --git a/config/template.config b/config/template.config
@@ -24,17 +24,16 @@ params {
         dest_reference_id = "hg38"
     }
 
-    // The source reference sequence (FASTA)
+    // The source reference sequence (FASTA). Must correspond with
+    // params.funcotator_data.src_reference_id
     src_fasta_ref = "/hot/ref/reference/GRCh37-EBI-hs37d5/hs37d5.fa"
-    // An identifier for the source sequence (e.g. hg19, hg38, b37). Only used to
-    // construct filenames.
 
-    // The destination reference sequence (FASTA)
+    // The destination reference sequence (FASTA). Must correspond with
+    // params.funcotator_data.dest_reference_id
     dest_fasta_ref = "/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta"
-    // An identifier for the destination sequence. This must be a valid
-    // subdirectory of the funcotator_source directory (e.g. hg19, hg38, b37)
-    dest_fasta_id = "hg38"
 
+    // The liftover chain file between the source and destination FASTAS
+    // references
     chain_file = "/hot/ref/tool-specific-input/liftOver/hg19ToHg38.over.chain"
 
     // FIXME Update to a stable path under /hot/ref/database

diff --git a/main.nf b/main.nf
@@ -17,36 +17,63 @@ include { workflow_extract_features} from './module/extract_features.nf'
 
 // Log info here
 log.info """\
-        ======================================
-        T E M P L A T E - N F  P I P E L I N E
-        ======================================
-        Boutros Lab
-
-        Current Configuration:
-        - pipeline:
-            name: ${workflow.manifest.name}
-            version: ${workflow.manifest.version}
-
-        - input:
-            input a: ${params.variable_name}
-            ...
-
-        - output:
-            output a: ${params.output_path}
-            ...
-
-        - options:
-            option a: ${params.option_name}
-            ...
-
-        Tools Used:
-            tool a: ${params.docker_image_name}
-
-        ------------------------------------
-        Starting workflow...
-        ------------------------------------
-        """
-        .stripIndent()
+    =====================================
+    S T A B L E L I F T   P I P E L I N E
+    =====================================
+    Boutros Lab
+
+    Current Configuration:
+    - pipeline:
+        name: ${workflow.manifest.name}
+        version: ${workflow.manifest.version}
+
+    - input:
+        dataset_id: ${params.dataset_id}
+        variant_caller: ${params.variant_caller}
+        rf_model: ${params.rf_model}
+
+        src_fasta_ref:   ${params.src_fasta_ref}
+        src_fasta_fai:   ${params.src_fasta_fai}
+        src_fasta_dict:  ${params.src_fasta_dict}
+
+        dest_fasta_ref:  ${params.dest_fasta_ref}
+        dest_fasta_fai:  ${params.dest_fasta_fai}
+        dest_fasta_dict: ${params.dest_fasta_dict}
+
+        chain_file: ${params.chain_file}
+        repeat_bed: ${params.repeat_bed}
+
+        funcotator_data:
+            data_source:       ${params.funcotator_data.data_source}
+            src_reference_id:  ${params.funcotator_data.src_reference_id}
+            dest_reference_id: ${params.funcotator_data.dest_reference_id}
+
+    - output:
+        output_dir_base: ${params.output_dir_base}
+
+    - options:
+        blcds_registered_dataset: ${params.blcds_registered_dataset}
+        ucla_cds: ${params.ucla_cds}
+
+        min_cpus: ${params.min_cpus}
+        max_cpus: ${params.max_cpus}
+
+        min_memory: ${params.min_memory}
+        max_memory: ${params.max_memory}
+
+    Tools Used:
+        BCFtools:   ${params.docker_image_bcftools}
+        BEDtools:   ${params.docker_image_bedtools}
+        PipeVal:    ${params.docker_image_pipeval}
+        SAMTools:   ${params.docker_image_samtools}
+        StableLift: ${params.docker_image_stablelift}
+        GATK:       ${params.docker_image_gatk}
+
+    ------------------------------------
+    Starting workflow...
+    ------------------------------------
+    """
+    .stripIndent()
 
 def indexFile(bam_or_vcf) {
     if(bam_or_vcf.endsWith('.bam')) {