From 36d345cacacec4fe11226ce3a3d4634c48f0e3a5 Mon Sep 17 00:00:00 2001
From: DLBPointon <damonlbp@hotmail.co.uk>
Date: Mon, 19 Feb 2024 10:23:17 +0000
Subject: [PATCH 1/2] Updates to the oncomplete and remove snapshot closes #263

---
 conf/base.config               |  5 -----
 workflows/treeval_rapid.nf     | 11 +----------
 workflows/treeval_rapid_tol.nf | 11 +----------
 3 files changed, 2 insertions(+), 25 deletions(-)

diff --git a/conf/base.config b/conf/base.config
index d5cd8a3f..24f3b355 100755
--- a/conf/base.config
+++ b/conf/base.config
@@ -153,11 +153,6 @@ process {
         memory  = { check_max( 1.GB     * task.attempt, 'memory' ) }
     }
 
-    withName: SNAPSHOT_HRES{
-        cpus    = { check_max( 6        * 1, 'cpus'              ) }
-        memory  = { check_max( 16.GB    * task.attempt, 'memory' ) }
-    }
-
     withName: PRETEXTMAP_STANDRD{
         cpus    = { check_max( 16       * 1, 'cpus'   ) }
         memory  = { check_max( 3.GB     * task.attempt, 'memory' ) }
diff --git a/workflows/treeval_rapid.nf b/workflows/treeval_rapid.nf
index 8ef15b86..390332a9 100755
--- a/workflows/treeval_rapid.nf
+++ b/workflows/treeval_rapid.nf
@@ -183,16 +183,7 @@ workflow TREEVAL_RAPID {
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-workflow.onComplete {
-    if (params.email || params.email_on_fail) {
-        NfcoreTemplate.email(workflow, params, summary_params, projectDir, log)
-    }
-
-    NfcoreTemplate.summary(workflow, params, log)
-    if (params.hook_url) {
-        NfcoreTemplate.IM_notification(workflow, params, summary_params, projectDir, log)
-    }
-}
+// PIPELINE ENTRYPOINT SUBWORKFLOWS WILL USE THE IMPLICIT ONCOMPLETE BLOCK
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
diff --git a/workflows/treeval_rapid_tol.nf b/workflows/treeval_rapid_tol.nf
index 1985c18a..dd41cd28 100755
--- a/workflows/treeval_rapid_tol.nf
+++ b/workflows/treeval_rapid_tol.nf
@@ -192,16 +192,7 @@ workflow TREEVAL_RAPID_TOL {
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-workflow.onComplete {
-    if (params.email || params.email_on_fail) {
-        NfcoreTemplate.email(workflow, params, summary_params, projectDir, log)
-    }
-
-    NfcoreTemplate.summary(workflow, params, log)
-    if (params.hook_url) {
-        NfcoreTemplate.IM_notification(workflow, params, summary_params, projectDir, log)
-    }
-}
+// PIPELINE ENTRYPOINT SUBWORKFLOWS WILL USE THE IMPLICIT ONCOMPLETE BLOCK
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

From a1820cfbb27ff2367657aa5a093377a384777dcb Mon Sep 17 00:00:00 2001
From: DLBPointon <damonlbp@hotmail.co.uk>
Date: Mon, 19 Feb 2024 10:40:54 +0000
Subject: [PATCH 2/2] Updates to the oncomplete and remove snapshot closes #263

---
 conf/modules.config | 7 +------
 1 file changed, 1 insertion(+), 6 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 21d876a7..938f27c0 100755
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -41,7 +41,7 @@ process {
 
     // Files to be used for pretext, likely to be deleted once the hic workflow is complete.
     // .bed, .hr.pretext, .lr.pretext, needs centromere}
-    withName: 'REFORMAT_INTERSECT|SEQTK_CUTN|GAP_LENGTH|PRETEXT_INGEST_HIRES|PRETEXT_INGEST_SNDRD|COOLER_ZOOMIFY|COV_FOLDER|UCSC_BEDGRAPHTOBIGWIG|BED2BW_NORMAL|BED2BW_LOG|EXTRACT_TELO|JUICER_TOOLS_PRE|SNAPSHOT_SRES|SNAPSHOT_HRES|PRETEXT_GRAPH' {
+    withName: 'REFORMAT_INTERSECT|SEQTK_CUTN|GAP_LENGTH|PRETEXT_INGEST_HIRES|PRETEXT_INGEST_SNDRD|COOLER_ZOOMIFY|COV_FOLDER|UCSC_BEDGRAPHTOBIGWIG|BED2BW_NORMAL|BED2BW_LOG|EXTRACT_TELO|JUICER_TOOLS_PRE|SNAPSHOT_SRES|PRETEXT_GRAPH' {
         publishDir = [
             path: { "${params.outdir}/hic_files" },
             mode: params.publish_dir_mode,
@@ -309,11 +309,6 @@ process {
         ext.prefix      = { "${meta.id}_normal" }
     }
 
-    withName: "SNAPSHOT_HRES" {
-        ext.args        = { "--sequences '=full' --resolution 1440 --texutureBuffer 1G" }
-        ext.prefix      = { "${meta.id}_hr" }
-    }
-
     withName: JUICER_TOOLS_PRE {
         ext.juicer_tools_jar    = "juicer_tools.1.8.9_jcuda.0.8.jar"
         ext.juicer_jvm_params   = "-Xms1g -Xmx36g"