From b76bc5dcb56ea80984c4562aed7ef56101bfa183 Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Thu, 24 Mar 2022 16:07:46 +0100
Subject: [PATCH 1/8] Post-release bump

---
 .github/workflows/ci.yml | 4 ++--
 CHANGELOG.md             | 2 +-
 Dockerfile               | 4 ++--
 environment.yml          | 2 +-
 nextflow.config          | 6 +++---
 5 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 508a6e0c4..afefa04c9 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -37,13 +37,13 @@ jobs:
 
       - name: Build new docker image
         if: env.MATCHED_FILES
-        run: docker build --no-cache . -t nfcore/eager:2.4.3
+        run: docker build --no-cache . -t nfcore/eager:dev
 
       - name: Pull docker image
         if: ${{ !env.MATCHED_FILES }}
         run: |
           docker pull nfcore/eager:dev
-          docker tag nfcore/eager:dev nfcore/eager:2.4.3
+          docker tag nfcore/eager:dev nfcore/eager:dev
 
       - name: Install Nextflow
         env:
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 0a59cb03c..687800a06 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -15,7 +15,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 - [#843](https://github.com/nf-core/eager/issues/843) Re-add direct piping of AdapterRemovalFixPrefix to pigz
 - [#844](https://github.com/nf-core/eager/issues/844) Fixed reference masking prior to pmdtools
 - [#845](https://github.com/nf-core/eager/issues/845) Updates parameter documention to specify `-s` preseq parameter also applies to lc_extrap
-- [#851](https://github.com/nf-core/eager/issues/851) Fixes a file-name clash during additional_library_merge, post-BAM trimming of different UDG treated libraries of a sample
+- [#851](https://github.com/nf-core/eager/issues/851) Fixes a file-name clash during additional_library_merge, post-BAM trimming of different UDG treated libraries of a sample (❤ to @alexandregilardet for reporting)
 - Renamed a range of MultiQC general stats table headers to improve clarity, documentation has been updated accordingly
 - [#857](https://github.com/nf-core/eager/issues/857) Corrected samtools fastq flag to _retain_ read-pair information when converting off-target BAM files to fastq in paired-end mapping (❤ to @alexhbnr for reporting)
 - [#866](https://github.com/nf-core/eager/issues/866) Fixed a typo in the indexing step of BWA mem when not-collapsing (❤ to @alexhbnr for reporting)
diff --git a/Dockerfile b/Dockerfile
index 865026492..612448539 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -7,7 +7,7 @@ COPY environment.yml /
 RUN conda env create --quiet -f /environment.yml && conda clean -a
 
 # Add conda installation dir to PATH (instead of doing 'conda activate')
-ENV PATH /opt/conda/envs/nf-core-eager-2.4.3/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-eager-2.4.4dev/bin:$PATH
 
 # Dump the details of the installed packages to a file for posterity
-RUN conda env export --name nf-core-eager-2.4.3 > nf-core-eager-2.4.3.yml
\ No newline at end of file
+RUN conda env export --name nf-core-eager-2.4.4dev > nf-core-eager-2.4.4dev.yml
\ No newline at end of file
diff --git a/environment.yml b/environment.yml
index ba9c1efe9..7531928b6 100644
--- a/environment.yml
+++ b/environment.yml
@@ -1,6 +1,6 @@
 # You can use this file to create a conda environment for this pipeline:
 #   conda env create -f environment.yml
-name: nf-core-eager-2.4.3
+name: nf-core-eager-2.4.4dev
 channels:
   - conda-forge
   - bioconda
diff --git a/nextflow.config b/nextflow.config
index 69ecad64d..35bf6af73 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -284,7 +284,7 @@ params {
 
 // Container slug. Stable releases should specify release tag!
 // Developmental code should specify :dev
-process.container = 'nfcore/eager:2.4.3'
+process.container = 'nfcore/eager:dev'
 
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'
@@ -414,7 +414,7 @@ manifest {
   description = 'A fully reproducible and state-of-the-art ancient DNA analysis pipeline'
   mainScript = 'main.nf'
   nextflowVersion = '>=20.07.1'
-  version = '2.4.3'
+  version = '2.4.4dev'
 }
 
 // Function to ensure that resource requirements don't go beyond
@@ -448,4 +448,4 @@ def check_max(obj, type) {
       return obj
     }
   }
-}
+}
\ No newline at end of file

From 30907e393fe723d89c2fdaf6ed3e4eea98bf7d9e Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Thu, 24 Mar 2022 16:08:43 +0100
Subject: [PATCH 2/8] Add new changelog section

---
 CHANGELOG.md | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 687800a06..c036a45b3 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,6 +3,16 @@
 The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
 
+## [dev]
+
+### `Added`
+
+### `Fixed`
+
+### `Dependencies`
+
+### `Deprecated`
+
 ## [2.4.3] - 2022-03-24
 
 ### `Added`

From 57764c0647a3aa86752e40ca9b509d9cf79f8f58 Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Tue, 5 Apr 2022 20:46:18 +0200
Subject: [PATCH 3/8] Change auxilary files from queue to value channels

---
 CHANGELOG.md |  2 ++
 main.nf      | 22 ++++++++++++----------
 2 files changed, 14 insertions(+), 10 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index c036a45b3..6e3c32c2c 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,6 +9,8 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 ### `Fixed`
 
+- Fixed some auxiliary files (adapater list, snpcapture/pileupcaller/sexdeterrmine BED files, and pileupCaller SNP file, PMD reference mask) in some cases only be used against one sample
+
 ### `Dependencies`
 
 ### `Deprecated`
diff --git a/main.nf b/main.nf
index d6d8ff03a..f5d38fe45 100644
--- a/main.nf
+++ b/main.nf
@@ -238,45 +238,47 @@ if ( !params.clip_adapters_list ) {
     Channel
       .fromPath("$projectDir/assets/nf-core_eager_dummy2.txt", checkIfExists: true)
       .ifEmpty { exit 1, "[nf-core/eager] error: adapters list file not found. Please check input. Supplied: --clip_adapters_list '${params.clip_adapters_list}'." }
+      .collect()
       .set {ch_adapterlist}
 } else {
     Channel
       .fromPath("${params.clip_adapters_list}", checkIfExists: true)
       .ifEmpty { exit 1, "[nf-core/eager] error: adapters list file not found. Please check input. Supplied: --clip_adapters_list '${params.clip_adapters_list}'." }
+      .collect()
       .set {ch_adapterlist}
 }
 
 if ( params.snpcapture_bed ) {
-    Channel.fromPath(params.snpcapture_bed, checkIfExists: true).set { ch_snpcapture_bed }
+    ch_snpcapture_bed = Channel.fromPath(params.snpcapture_bed, checkIfExists: true).collect()
 } else {
-    Channel.fromPath("$projectDir/assets/nf-core_eager_dummy.txt").set { ch_snpcapture_bed }
+    ch_snpcapture_bed = Channel.fromPath("$projectDir/assets/nf-core_eager_dummy.txt").collect()
 }
 
 // Set up channel with pmdtools reference mask bedfile
 if (!params.pmdtools_reference_mask) {
-  ch_bedfile_for_reference_masking = Channel.fromPath("$projectDir/assets/nf-core_eager_dummy.txt")
+  ch_bedfile_for_reference_masking = Channel.fromPath("$projectDir/assets/nf-core_eager_dummy.txt").collect()
 } else {
-  ch_bedfile_for_reference_masking = Channel.fromPath(params.pmdtools_reference_mask, checkIfExists: true)
+  ch_bedfile_for_reference_masking = Channel.fromPath(params.pmdtools_reference_mask, checkIfExists: true).collect()
 }
 
 // SexDetermination channel set up and bedfile validation
 if (!params.sexdeterrmine_bedfile) {
-  ch_bed_for_sexdeterrmine = Channel.fromPath("$projectDir/assets/nf-core_eager_dummy.txt")
+  ch_bed_for_sexdeterrmine = Channel.fromPath("$projectDir/assets/nf-core_eager_dummy.txt").collect()
 } else {
-  ch_bed_for_sexdeterrmine = Channel.fromPath(params.sexdeterrmine_bedfile, checkIfExists: true)
+  ch_bed_for_sexdeterrmine = Channel.fromPath(params.sexdeterrmine_bedfile, checkIfExists: true).collect()
 }
 
  // pileupCaller channel generation and input checks for 'random sampling' genotyping
 if (!params.pileupcaller_bedfile) {
-  ch_bed_for_pileupcaller = Channel.fromPath("$projectDir/assets/nf-core_eager_dummy.txt")
+  ch_bed_for_pileupcaller = Channel.fromPath("$projectDir/assets/nf-core_eager_dummy.txt").collect()
 } else {
-  ch_bed_for_pileupcaller = Channel.fromPath(params.pileupcaller_bedfile, checkIfExists: true)
+  ch_bed_for_pileupcaller = Channel.fromPath(params.pileupcaller_bedfile, checkIfExists: true).collect()
 }
 
 if (!params.pileupcaller_snpfile) {
-  ch_snp_for_pileupcaller = Channel.fromPath("$projectDir/assets/nf-core_eager_dummy2.txt")
+  ch_snp_for_pileupcaller = Channel.fromPath("$projectDir/assets/nf-core_eager_dummy2.txt").collect()
 } else {
-  ch_snp_for_pileupcaller = Channel.fromPath(params.pileupcaller_snpfile, checkIfExists: true)
+  ch_snp_for_pileupcaller = Channel.fromPath(params.pileupcaller_snpfile, checkIfExists: true).collect()
 }
 
 // Create input channel for MALT database directory, checking directory exists

From 43db446b2f465f3b1503f0a6dfc16384c5c1b84c Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Tue, 5 Apr 2022 20:50:06 +0200
Subject: [PATCH 4/8] New style changelog

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6e3c32c2c..6c93ccc00 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,7 +9,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 ### `Fixed`
 
-- Fixed some auxiliary files (adapater list, snpcapture/pileupcaller/sexdeterrmine BED files, and pileupCaller SNP file, PMD reference mask) in some cases only be used against one sample
+- Fixed some auxiliary files (adapater list, snpcapture/pileupcaller/sexdeterrmine BED files, and pileupCaller SNP file, PMD reference mask) in some cases only be used against one sample (❤ to @meganemichel for reporting, fix by @jfy133)
 
 ### `Dependencies`
 

From a76eefb59198a9cb08018fc3d84325903c6af712 Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Wed, 6 Apr 2022 08:20:50 +0200
Subject: [PATCH 5/8] Bump version for patch

---
 .github/workflows/ci.yml | 4 ++--
 Dockerfile               | 4 ++--
 environment.yml          | 2 +-
 nextflow.config          | 4 ++--
 4 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index afefa04c9..8977cd31e 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -37,13 +37,13 @@ jobs:
 
       - name: Build new docker image
         if: env.MATCHED_FILES
-        run: docker build --no-cache . -t nfcore/eager:dev
+        run: docker build --no-cache . -t nfcore/eager:2.4.4
 
       - name: Pull docker image
         if: ${{ !env.MATCHED_FILES }}
         run: |
           docker pull nfcore/eager:dev
-          docker tag nfcore/eager:dev nfcore/eager:dev
+          docker tag nfcore/eager:dev nfcore/eager:2.4.4
 
       - name: Install Nextflow
         env:
diff --git a/Dockerfile b/Dockerfile
index 612448539..30ec3701e 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -7,7 +7,7 @@ COPY environment.yml /
 RUN conda env create --quiet -f /environment.yml && conda clean -a
 
 # Add conda installation dir to PATH (instead of doing 'conda activate')
-ENV PATH /opt/conda/envs/nf-core-eager-2.4.4dev/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-eager-2.4.4/bin:$PATH
 
 # Dump the details of the installed packages to a file for posterity
-RUN conda env export --name nf-core-eager-2.4.4dev > nf-core-eager-2.4.4dev.yml
\ No newline at end of file
+RUN conda env export --name nf-core-eager-2.4.4 > nf-core-eager-2.4.4.yml
\ No newline at end of file
diff --git a/environment.yml b/environment.yml
index 7531928b6..05acf03b2 100644
--- a/environment.yml
+++ b/environment.yml
@@ -1,6 +1,6 @@
 # You can use this file to create a conda environment for this pipeline:
 #   conda env create -f environment.yml
-name: nf-core-eager-2.4.4dev
+name: nf-core-eager-2.4.4
 channels:
   - conda-forge
   - bioconda
diff --git a/nextflow.config b/nextflow.config
index 35bf6af73..86747172b 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -284,7 +284,7 @@ params {
 
 // Container slug. Stable releases should specify release tag!
 // Developmental code should specify :dev
-process.container = 'nfcore/eager:dev'
+process.container = 'nfcore/eager:2.4.4'
 
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'
@@ -414,7 +414,7 @@ manifest {
   description = 'A fully reproducible and state-of-the-art ancient DNA analysis pipeline'
   mainScript = 'main.nf'
   nextflowVersion = '>=20.07.1'
-  version = '2.4.4dev'
+  version = '2.4.4'
 }
 
 // Function to ensure that resource requirements don't go beyond

From 86111a14b18c56674e1efe7e7bc0360e7bd44ed8 Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Wed, 6 Apr 2022 21:47:00 +0200
Subject: [PATCH 6/8] Update CHANGELOG.md

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6c93ccc00..8290a0fe5 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
 
-## [dev]
+## [2.4.4] - 2020-04-07
 
 ### `Added`
 

From 6875451f4a3f24715b8fa7214fe96db1f2dbddb7 Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Wed, 6 Apr 2022 21:47:17 +0200
Subject: [PATCH 7/8] Update CHANGELOG.md

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 8290a0fe5..34579ec6d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
 
-## [2.4.4] - 2020-04-07
+## [2.4.4] - 2022-04-07
 
 ### `Added`
 

From 197f6a735d96a28ea40c6b67fe448925b0a615a0 Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Fri, 8 Apr 2022 21:15:59 +0200
Subject: [PATCH 8/8] Update CHANGELOG.md

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 34579ec6d..d31df3f8b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
 
-## [2.4.4] - 2022-04-07
+## [2.4.4] - 2022-04-08
 
 ### `Added`