Addition of indicator files, these are saved to the main outdir

sanger-tol · Aug 9, 2024 · dfdbb8d · dfdbb8d
1 parent 0bbd384
commit dfdbb8d
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Showing 4 changed files with 56 additions and 2 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -31,6 +31,21 @@ process {
         ]
     }
 
+    withName: AUTOFILTER_AND_CHECK_ASSEMBLY {
+        publishDir = [
+            path: { "${params.outdir}/" },
+            mode: params.publish_dir_mode,
+            pattern: "autofiltering_done_indicator_file.txt"
+        ]
+    }
+
+    withName: GenIndicator {
+        publishDir = [
+            path: { "${params.outdir}/" },
+            mode: params.publish_dir_mode
+        ]
+    }
+
     withName: ASCC_MERGE_TABLES {
         publishDir = [
             path: { "${params.outdir}/ASCC-main-output" },

diff --git a/modules/local/autofiltering.nf b/modules/local/autofiltering.nf
@@ -18,7 +18,7 @@ process AUTOFILTER_AND_CHECK_ASSEMBLY {
     tuple val(meta), path("ABNORMAL_CHECK.csv"),                        emit: fcs_tiara_summary
     tuple val(meta), path("assembly_filtering_removed_sequences.txt"),  emit: removed_seqs
     path("fcs-gx_alarm_indicator_file.txt"),                            emit: alarm_file
-    //path("autofiltering_done_indicator_file.txt"),                      emit: indicator_file
+    path("autofiltering_done_indicator_file.txt"),                      emit: indicator_file
     path "versions.yml",                                                emit: versions
 
     script:
@@ -39,7 +39,7 @@ process AUTOFILTER_AND_CHECK_ASSEMBLY {
     # The below indicator file is used in Sanger-Tol to allow for other processes
     # to begin once generated. This allows us to speed up the overall flow of the
     # Tol-engine
-    touch ${params.outdir}/autofiltering_done_indicator_file.txt
+    touch autofiltering_done_indicator_file.txt
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/nextflow.config b/nextflow.config
@@ -15,6 +15,13 @@ params {
     outdir                     = "${params.outdir}"
     tracedir                   = "${params.outdir}/pipeline_info/"
 
+    // MultiQC options
+    multiqc_config             = null
+    multiqc_title              = null
+    multiqc_logo               = null
+    max_multiqc_email_size     = '25.MB'
+    multiqc_methods_description = null
+
     // Boilerplate options
     outdir                     = null
     publish_dir_mode           = 'copy'

diff --git a/workflows/ascc.nf b/workflows/ascc.nf
@@ -451,6 +451,7 @@ workflow ASCC {
             YAML_INPUT.out.ncbi_rankedlineage_path
         )
         ch_autofilt_assem   = AUTOFILTER_AND_CHECK_ASSEMBLY.out.decontaminated_assembly.map{it[1]}
+        ch_autofilt_indicator = AUTOFILTER_AND_CHECK_ASSEMBLY.out.indicator_file
 
         AUTOFILTER_AND_CHECK_ASSEMBLY.out.alarm_file
             .map { file -> file.text.trim() }
@@ -464,6 +465,7 @@ workflow ASCC {
         ch_versions         = ch_versions.mix(AUTOFILTER_AND_CHECK_ASSEMBLY.out.versions)
     } else {
         ch_autofilt_assem   = []
+        ch_autofilt_indicator = []
     }
 
     //
@@ -537,6 +539,15 @@ workflow ASCC {
     ch_versions             = ch_versions.mix(ASCC_MERGE_TABLES.out.versions)
 
 
+    GenIndicator (
+        ch_autofilt_indicator,
+        ch_fcsgx,
+        ch_fcsadapt,
+        ch_tiara,
+        ch_vecscreen,
+        ch_barcode,
+    )
+
 
     //
     // SUBWORKFLOW: Collates version data from prior subworflows
@@ -565,6 +576,27 @@ process GrabFiles {
     "true"
 }
 
+process GenIndicator {
+    label 'process_tiny'
+
+    tag "Generating Phase 1 Indicator"
+    executor 'local'
+
+    input:
+    val(a)
+    val(b)
+    val(c)
+    val(d)
+    val(e)
+    val(f)
+
+    output:
+    path("decon_first_stage_done_indicator_file.txt")
+
+    script:
+    "touch decon_first_stage_done_indicator_file.txt"
+}
+
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     COMPLETION EMAIL AND SUMMARY