From ac3a82615efe397454e97818aa50e1b6e27e2c7b Mon Sep 17 00:00:00 2001
From: Laura Blum <lblum@neb.com>
Date: Fri, 9 Jan 2026 14:46:54 -0500
Subject: [PATCH 1/4] make it possible to supply a local fastp path

---
 modules/fastp.nf | 3 ++-
 nextflow.config  | 3 ++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/modules/fastp.nf b/modules/fastp.nf
index e401773..fb38b1f 100644
--- a/modules/fastp.nf
+++ b/modules/fastp.nf
@@ -14,6 +14,7 @@ process fastp {
         tuple val("${task.process}"), val('fastp'), eval('fastp --version 2>&1 | cut -f 2 -d " "'), topic: versions
     
     script:
+    def fastp_path = params.fastp_path ? params.fastp_path : ''
     def fastp_args = params.single_end ? "--out1 ${library}.1.trimmed.fastq.gz" : "--interleaved_in --out1 ${library}.1.trimmed.fastq.gz --out2 ${library}.2.trimmed.fastq.gz"
     """
     set +o pipefail
@@ -24,7 +25,7 @@ process fastp {
     echo \${trim_polyg} | awk '{ if (length(\$1)>0) { print "2-color instrument: poly-g trim mode on" } }'
     
     samtools fastq -n ${bam} | \\
-    fastp --stdin \\
+    ${fastp_path}fastp --stdin \\
                     -l 2 -Q \${trim_polyg} \\
                     --thread 1 \\
                     --overrepresentation_analysis \\
diff --git a/nextflow.config b/nextflow.config
index 91db943..27f9d13 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -24,6 +24,7 @@ params {
     // NEB only
     path_to_ngs_agg           = null
     workflow_name_modifier    = null
+    fastp_path                = null 
 
 }
 
@@ -70,7 +71,7 @@ profiles {
     test { 
         includeConfig 'conf/test.config'
         conda.enabled          = true
-        conda.useMicromamba    = true
+        //conda.useMicromamba    = true
         conda.cacheDir         = "${projectDir}/.conda/envs"
     }
 }

From c2911e4102607d8b8557de3afae353e1827c3c9f Mon Sep 17 00:00:00 2001
From: Laura Blum <lblum@neb.com>
Date: Fri, 9 Jan 2026 15:19:48 -0500
Subject: [PATCH 2/4] so snapshots match

---
 conf/test.config | 1 +
 1 file changed, 1 insertion(+)

diff --git a/conf/test.config b/conf/test.config
index 734ff99..a06664f 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -24,6 +24,7 @@ params {
     max_time   = '6.h'
 
     outputDir = "test_output"
+    fastp_path = null
 
     }
 

From c29c30fc96ec650a0171a38f6f46a788d9157ebc Mon Sep 17 00:00:00 2001
From: Laura Blum <lblum@neb.com>
Date: Fri, 9 Jan 2026 15:49:38 -0500
Subject: [PATCH 3/4] this would override if we pass it in via seq shepherd
 config

---
 nextflow.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nextflow.config b/nextflow.config
index 27f9d13..da0f832 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -24,7 +24,7 @@ params {
     // NEB only
     path_to_ngs_agg           = null
     workflow_name_modifier    = null
-    fastp_path                = null 
+    //fastp_path                = null 
 
 }
 

From 99ad6e6a1bd667ff39a098d302de568c98d11eea Mon Sep 17 00:00:00 2001
From: Laura Blum <lblum@neb.com>
Date: Fri, 9 Jan 2026 15:57:55 -0500
Subject: [PATCH 4/4] remove comments

---
 nextflow.config | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/nextflow.config b/nextflow.config
index da0f832..91db943 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -24,7 +24,6 @@ params {
     // NEB only
     path_to_ngs_agg           = null
     workflow_name_modifier    = null
-    //fastp_path                = null 
 
 }
 
@@ -71,7 +70,7 @@ profiles {
     test { 
         includeConfig 'conf/test.config'
         conda.enabled          = true
-        //conda.useMicromamba    = true
+        conda.useMicromamba    = true
         conda.cacheDir         = "${projectDir}/.conda/envs"
     }
 }