From d2222cea9c7244b6a7ec8401f3a20125a80cb007 Mon Sep 17 00:00:00 2001
From: Andrea Sboner <asboner@gmail.com>
Date: Fri, 23 Oct 2020 23:50:25 -0400
Subject: [PATCH] Parametrized input pattern search

---
 README.md       | 15 ++++++++-------
 main.nf         |  2 +-
 nextflow.config |  1 +
 3 files changed, 10 insertions(+), 8 deletions(-)

diff --git a/README.md b/README.md
index c325b0f..ae227d1 100644
--- a/README.md
+++ b/README.md
@@ -75,14 +75,15 @@ To run this pipeline using [Nextflow](https://www.nextflow.io/), simply run the
 where `nextflow.config` include the minimum set of parameters to run ERVmap within the docker container. Specifically:
 ```
 params {
-    genome='/path/to/genome' # external path to the indexed genome for the STAR aligner
-    inputDir='path/to/input/folder' # external path of the input data
-    outputDir='/path/to/output/folder' # external path of the output results
+    genome='/path/to/genome'               # external path to the indexed genome for the STAR aligner
+    inputDir='path/to/input/folder'        # external path of the input data
+    inputPattern="*{1,2}.fastq.gz"         # pattern to search for input FASTQ files
+    outputDir='/path/to/output/folder'     # external path of the output results
     starTmpDir='/path/to/STAR/temp/folder' # external path of the STAR aligner temporary folder. REQUIRED
-    localOutDir='.' # internal path of the results
-    cpus=20 # Number of cpus/threads to use for the alignment 
-    limitMemory=1850861158 # memory limit for STAR
-    debug='off' # either [on|off] 
+    localOutDir='.'                        # internal path of the results
+    cpus=20                                # Number of cpus/threads to use for the alignment 
+    limitMemory=1850861158                 # memory limit for STAR
+    debug='off'                            # either [on|off] 
 }
 ```
 **NOTE:** Adjust the memory settings of the docker container if needed, but recall that STAR requires about 32G of RAM (see [Optional Parameters](#optparam)).
diff --git a/main.nf b/main.nf
index e76544f..949d30a 100644
--- a/main.nf
+++ b/main.nf
@@ -26,7 +26,7 @@ if (!params.debug) {
 }
 
 
-pairFiles_ch = Channel.fromFilePairs( params.inputDir+"/*{1,2}.fastq.gz", size: 2, checkIfExists: true )
+pairFiles_ch = Channel.fromFilePairs( params.inputDir+"/"+params.inputPattern, size: 2, checkIfExists: true )
 
 
 process ERValign {
diff --git a/nextflow.config b/nextflow.config
index 7909da0..79dccf8 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -11,6 +11,7 @@ docker {
 params {
     genome='/path/to/genome'
     inputDir='path/to/input/folder'
+    inputPattern="*{1,2}.fastq.gz"
     outputDir='/path/to/output/folder'
     starTmpDir='/path/to/STAR/temp/folder'
     localOutDir='.'