From 7dcbbaceb6fc46243bce1a1c63ab1f1abfc7d63f Mon Sep 17 00:00:00 2001
From: DSchreyer <daniel-schreyer@web.de>
Date: Mon, 26 Jun 2023 11:02:32 +0100
Subject: [PATCH 1/3] Collect fix -> Pipeline works again with all samples. Not
 only first sample

---
 workflows/circdna.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/workflows/circdna.nf b/workflows/circdna.nf
index d8e73704..6dd647e6 100644
--- a/workflows/circdna.nf
+++ b/workflows/circdna.nf
@@ -23,7 +23,7 @@ if (!(params.input_format == "FASTQ" | params.input_format == "BAM")) {
 }
 
 // Modify fasta channel to include meta data
-ch_fasta_meta = ch_fasta.map{ it -> [[id:it[0].baseName], it] }
+ch_fasta_meta = ch_fasta.map{ it -> [[id:it[0].baseName], it] }.collect()
 
 branch = params.circle_identifier.split(",")
 run_circexplorer2 = ("circexplorer2" in branch)

From 843ea15a561b1dbb4e93c41e4b637dc215491325 Mon Sep 17 00:00:00 2001
From: DSchreyer <daniel-schreyer@web.de>
Date: Mon, 26 Jun 2023 11:06:05 +0100
Subject: [PATCH 2/3] relase 1.0.4

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

diff --git a/nextflow.config b/nextflow.config
index 62206027..7eed736f 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -261,7 +261,7 @@ manifest {
     description     = """Pipeline for the identification of circular DNAs"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=22.10.1'
-    version         = '1.0.3'
+    version = '1.0.4'
     doi             = '10.5281/zenodo.7712010'
 }
 

From 621bef1422cc958619775374adc648154b3e5f4e Mon Sep 17 00:00:00 2001
From: DSchreyer <daniel-schreyer@web.de>
Date: Mon, 26 Jun 2023 11:06:50 +0100
Subject: [PATCH 3/3] Updated Changelog

---
 CHANGELOG.md | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 01a019c1..fcbcdbdf 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,6 +3,18 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## v1.0.4 - [2023-06-26]
+
+### `Added`
+
+### `Fixed`
+
+- Bug that the pipeline only runs with one sample when Picard Markduplicates is used
+
+### `Dependencies`
+
+### `Deprecated`
+
 ## v1.0.3 - [2023-05-26]
 
 ### `Added`