removed module tests

phac-nml · Apr 2, 2024 · f4d2887 · f4d2887
1 parent 40e41c8
commit f4d2887
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Showing 11 changed files with 148 additions and 238 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -15,8 +15,11 @@ process {
     // Publish directory names
     assembly_directory_name = "assembly"
     summary_directory_name = "summary"
+    profile_dists_directory_name = "distances"
+    gas_call_directory_name = "call"
 
-    locidex_merge_directory_name = [params.outdir , "locidex", "merge"].join(File.separator)
+    locidex_merge_ref_directory_name = [params.outdir , "locidex", "merge", "reference"].join(File.separator)
+    locidex_merge_query_directory_name = [params.outdir , "locidex", "merge", "query"].join(File.separator)
 
     publishDir = [
         path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
@@ -56,15 +59,55 @@ process {
         ]
     }
 
-    withName: LOCIDEX_MERGE {
+    withName: LOCIDEX_MERGE_REF {
         publishDir = [
-            path: locidex_merge_directory_name,
+            path: locidex_merge_ref_directory_name,
             mode: params.publish_dir_mode,
             pattern:  "*/*",
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
+    withName: LOCIDEX_MERGE_QUERY {
+        publishDir = [
+            path: locidex_merge_query_directory_name,
+            mode: params.publish_dir_mode,
+            pattern:  "*/*",
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+
+    withName: PROFILE_DISTS {
+        publishDir = [
+            path: { ["${params.outdir}", "${task.profile_dists_directory_name}"].join(File.separator) },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null :
+                filename.contains(File.separator) ? filename.split(File.separator)[-1] : filename }
+        ]
+    }
+
+    withName: GAS_CALL {
+        publishDir = [
+            [
+                path: { ["${params.outdir}", "${task.gas_call_directory_name}"].join(File.separator) },
+                mode: params.publish_dir_mode,
+                pattern: "*/thresholds.json"
+            ],
+            [
+                path: { ["${params.outdir}", "${task.gas_call_directory_name}"].join(File.separator) },
+                mode: params.publish_dir_mode,
+                pattern: "*/results.{text,parquet}"
+            ],
+            [
+                path: { ["${params.outdir}", "${task.gas_call_directory_name}"].join(File.separator) },
+                mode: params.publish_dir_mode,
+                pattern: "*/run.json"
+            ]
+        ]
+    }
+
+
     withName: CUSTOM_DUMPSOFTWAREVERSIONS {
         publishDir = [
             path: { "${params.outdir}/pipeline_info" },

diff --git a/modules/local/gas/call/main.nf b/modules/local/gas/call/main.nf
@@ -2,25 +2,26 @@
 
 process GAS_CALL{
     label "process_high"
-    tag "Calling: ${meta.id}"
+    tag "Assigning Nomenclature"
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/genomic_address_service%3A0.1.1--pyh7cba7a3_1' :
         'quay.io/biocontainers/genomic_address_service:0.1.1--pyh7cba7a3_1' }"
 
 
     input:
-    tuple val(meta), path(reference_clusters), path(distances)
+    path(reference_clusters)
+    path(distances)
 
     output:
-    tuple val(meta), path("${prefix}/results.{text,parquet}"), emit: distances, optional: true
-    tuple val(meta), path("${prefix}/thresholds.json"), emit: thresholds
-    tuple val(meta), path("${prefix}/run.json"), emit: run
+    path("${prefix}/results.{text,parquet}"), emit: distances, optional: true
+    path("${prefix}/thresholds.json"), emit: thresholds
+    path("${prefix}/run.json"), emit: run
     path  "versions.yml", emit: versions
 
     script:
     // Need to add more args for gas call below
-    prefix = meta.id
+    prefix = "Called"
     """
     gas call --dists $distances \\
                 --rclusters $reference_clusters \\

diff --git a/modules/local/locidex/merge/main.nf b/modules/local/locidex/merge/main.nf
@@ -9,17 +9,19 @@ process LOCIDEX_MERGE {
     'quay.io/biocontainers/locidex:0.1.1--pyhdfd78af_0' }"
 
     input:
-    val input_values // [file(sample1), file(sample2), file(sample3), etc...]
+    path input_values // [file(sample1), file(sample2), file(sample3), etc...]
+    val input_tag // makes output unique and denotes the item as the reference or query to preven name collision
 
     output:
     path("${combined_dir}/*.tsv"), emit: combined_profiles
-    path("${combined_dir}/*.json"), emit: report
     path "versions.yml", emit: versions
 
     script:
-    combined_dir = "merged"
+    combined_dir = "merged_${input_tag}"
     """
     locidex merge -i ${input_values.join(' ')} -o ${combined_dir}
+
+    mv ${combined_dir}/*.tsv ${combined_dir}/merged_profiles_${input_tag}.tsv
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         locidex merge: \$(echo \$(locidex search -V 2>&1) | sed 's/^.*locidex //' )

diff --git a/modules/local/profile_dists/main.nf b/modules/local/profile_dists/main.nf
@@ -1,24 +1,25 @@
 process PROFILE_DISTS{
     label "process_high"
-    tag "Pairwise Distance Generation: ${meta.id}"
+    tag "Gathering Distances Between Reference and Query Profiles"
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/profile_dists%3A1.0.0--pyh7cba7a3_0' :
         'quay.io/biocontainers/profile_dists:1.0.0--pyh7cba7a3_0' }"
 
     input:
-    tuple val(meta), path(query), path(ref)
+    path query
+    path ref
     val mapping_format
-    path(mapping_file)
-    path(columns)
+    path mapping_file
+    path columns
 
 
     output:
-    tuple val(meta), path("${prefix}_${mapping_format}/allele_map.json"), emit: allele_map
-    tuple val(meta), path("${prefix}_${mapping_format}/query_profile.{text,parquet}"), emit: query_profile
-    tuple val(meta), path("${prefix}_${mapping_format}/ref_profile.{text,parquet}"), emit: ref_profile
-    tuple val(meta), path("${prefix}_${mapping_format}/results.{text,parquet}"), emit: results
-    tuple val(meta), path("${prefix}_${mapping_format}/run.json"), emit: run
+    path("${prefix}/allele_map.json"), emit: allele_map
+    path("${prefix}/query_profile.{text,parquet}"), emit: query_profile
+    path("${prefix}/ref_profile.{text,parquet}"), emit: ref_profile
+    path("${prefix}/results.{text,parquet}"), emit: results
+    path("${prefix}/run.json"), emit: run
     path  "versions.yml", emit: versions
 
 
@@ -41,7 +42,7 @@ process PROFILE_DISTS{
         args = args + " --count_missing"
     }
     // --match_threshold $params.profile_dists.match_thresh \\
-    prefix = meta.id
+    prefix = "distances_${mapping_format}"
     """
     profile_dists --query $query --ref $ref $args --outfmt $mapping_format \\
                 --distm $params.pd_distm \\
@@ -50,7 +51,7 @@ process PROFILE_DISTS{
                 --sample_qual_thresh $params.pd_sample_quality_threshold \\
                 --max_mem ${task.memory.toGiga()} \\
                 --cpus ${task.cpus} \\
-                -o ${prefix}_${mapping_format}
+                -o ${prefix}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/nextflow.config b/nextflow.config
@@ -47,6 +47,23 @@ params {
     validate_params                  = true
 
     // Profile Dists
+    pd_outfmt = "pairwise"
+    pd_distm = "scaled"
+    pd_missing_threshold = 1.0
+    pd_sample_quality_threshold = 1.0
+    pd_match_threshold = -1.0
+    pd_file_type = "text"
+    pd_mapping_file = null // default is no file
+    pd_force = false
+    pd_skip = false
+    pd_columns = null
+    pd_count_missing = true
+
+
+    // GAS Call
+    gm_thresholds = "10,5,0"
+    gm_delimiter = "'.'" // note the single quotes surrounding the delimiter
+    ref_clusters = ""
 
 }
 

diff --git a/tests/modules/local/assemblystub/main.nf.test b/tests/modules/local/assemblystub/main.nf.test
diff --git a/tests/modules/local/generatesamplejson/main.nf.test b/tests/modules/local/generatesamplejson/main.nf.test
diff --git a/tests/modules/local/generatesummary/main.nf.test b/tests/modules/local/generatesummary/main.nf.test
diff --git a/tests/modules/local/iridanextoutput/main.nf.test b/tests/modules/local/iridanextoutput/main.nf.test