From a814dafa80deac036a8c881031a0672a40881596 Mon Sep 17 00:00:00 2001
From: melferink <m.elferink@umcutrecht.nl>
Date: Wed, 19 Apr 2023 10:27:01 +0200
Subject: [PATCH 1/7] first commit

---
 Sambamba/0.7.0/SubSample.nf | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)
 create mode 100644 Sambamba/0.7.0/SubSample.nf

diff --git a/Sambamba/0.7.0/SubSample.nf b/Sambamba/0.7.0/SubSample.nf
new file mode 100644
index 00000000..6af816d9
--- /dev/null
+++ b/Sambamba/0.7.0/SubSample.nf
@@ -0,0 +1,18 @@
+process SubSample {
+    tag {"Sambamba SubSample ${sample_id}"}
+    label 'Sambamba_0_7_0'
+    label 'Sambamba_0_7_0_SubSample'
+    container = 'quay.io/biocontainers/sambamba:0.7.0--h89e63da_1'
+    shell = ['/bin/bash', '-euo', 'pipefail']
+
+    input:
+        tuple(sample_id, val(faction), path(bam_file), path(bai_file))
+
+    output:
+        tuple(sample_id, path("${bam_file.baseName}.subsample.bam"), path("${bam_file.baseName}.subsample.bam.bai"), emit: subsample_bam_file)
+
+    script:
+        """
+        sambamba view -t ${task.cpus} -f bam -s ${faction} ${params.optional} ${bam_file} -o ${bam_file.baseName}.subsample.bam
+        """
+}

From fbe13797f078817d9ca384f84a591be27a788505 Mon Sep 17 00:00:00 2001
From: melferink <m.elferink@umcutrecht.nl>
Date: Wed, 19 Apr 2023 10:27:11 +0200
Subject: [PATCH 2/7] first commit

---
 Mosdepth/0.3.3/Mosdepth.nf | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)
 create mode 100644 Mosdepth/0.3.3/Mosdepth.nf

diff --git a/Mosdepth/0.3.3/Mosdepth.nf b/Mosdepth/0.3.3/Mosdepth.nf
new file mode 100644
index 00000000..4f2aa056
--- /dev/null
+++ b/Mosdepth/0.3.3/Mosdepth.nf
@@ -0,0 +1,17 @@
+process Mosdepth {
+    tag {"Mosdepth ${sample_id}"}
+    label 'Mosdepth_0_3_3'
+    container = 'quay.io/biocontainers/mosdepth:0.3.3--h37c5b7d_2'
+    shell = ['/bin/bash', '-euo', 'pipefail']
+
+    input:
+        tuple(val(sample_id), path(bam_file), path(bai_file))
+
+    output:
+        tuple(sample_id, path("${sample_id}.mosdepth.summary.txt"))
+
+    script:
+        """
+        mosdepth -t ${task.cpus} ${params.optional} ${sample_id} ${bam_file}
+        """
+}

From 84e7c0e29cd6529797cafe625e33ca4368b0cdf0 Mon Sep 17 00:00:00 2001
From: melferink <m.elferink@umcutrecht.nl>
Date: Thu, 20 Apr 2023 12:48:25 +0200
Subject: [PATCH 3/7] renamed

---
 Sambamba/0.7.0/SubSample.nf | 18 ------------------
 1 file changed, 18 deletions(-)
 delete mode 100644 Sambamba/0.7.0/SubSample.nf

diff --git a/Sambamba/0.7.0/SubSample.nf b/Sambamba/0.7.0/SubSample.nf
deleted file mode 100644
index 6af816d9..00000000
--- a/Sambamba/0.7.0/SubSample.nf
+++ /dev/null
@@ -1,18 +0,0 @@
-process SubSample {
-    tag {"Sambamba SubSample ${sample_id}"}
-    label 'Sambamba_0_7_0'
-    label 'Sambamba_0_7_0_SubSample'
-    container = 'quay.io/biocontainers/sambamba:0.7.0--h89e63da_1'
-    shell = ['/bin/bash', '-euo', 'pipefail']
-
-    input:
-        tuple(sample_id, val(faction), path(bam_file), path(bai_file))
-
-    output:
-        tuple(sample_id, path("${bam_file.baseName}.subsample.bam"), path("${bam_file.baseName}.subsample.bam.bai"), emit: subsample_bam_file)
-
-    script:
-        """
-        sambamba view -t ${task.cpus} -f bam -s ${faction} ${params.optional} ${bam_file} -o ${bam_file.baseName}.subsample.bam
-        """
-}

From de8672a6026cc3234a32ad788199b2273a166ce8 Mon Sep 17 00:00:00 2001
From: melferink <m.elferink@umcutrecht.nl>
Date: Thu, 20 Apr 2023 12:48:35 +0200
Subject: [PATCH 4/7] renamed

---
 Sambamba/0.7.0/ViewSubsample.nf | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)
 create mode 100644 Sambamba/0.7.0/ViewSubsample.nf

diff --git a/Sambamba/0.7.0/ViewSubsample.nf b/Sambamba/0.7.0/ViewSubsample.nf
new file mode 100644
index 00000000..5e87496d
--- /dev/null
+++ b/Sambamba/0.7.0/ViewSubsample.nf
@@ -0,0 +1,18 @@
+process Subsample {
+    tag {"Sambamba Subsample ${sample_id}"}
+    label 'Sambamba_0_7_0'
+    label 'Sambamba_0_7_0_ViewSubsample'
+    container = 'quay.io/biocontainers/sambamba:0.7.0--h89e63da_1'
+    shell = ['/bin/bash', '-euo', 'pipefail']
+
+    input:
+        tuple(sample_id, val(faction), path(bam_file), path(bai_file))
+
+    output:
+        tuple(sample_id, path("${bam_file.baseName}.subsample.bam"), path("${bam_file.baseName}.subsample.bam.bai"), emit: subsample_bam_file)
+
+    script:
+        """
+        sambamba view -t ${task.cpus} -f bam -s ${faction} ${params.optional} ${bam_file} -o ${bam_file.baseName}.subsample.bam
+        """
+}

From 762960fbe10616cda95f73fc5740dde07bb76589 Mon Sep 17 00:00:00 2001
From: melferink <m.elferink@umcutrecht.nl>
Date: Tue, 2 May 2023 13:21:47 +0200
Subject: [PATCH 5/7] fixed typo

---
 Sambamba/0.7.0/ViewSubsample.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/Sambamba/0.7.0/ViewSubsample.nf b/Sambamba/0.7.0/ViewSubsample.nf
index 5e87496d..88ddf5ad 100644
--- a/Sambamba/0.7.0/ViewSubsample.nf
+++ b/Sambamba/0.7.0/ViewSubsample.nf
@@ -6,13 +6,13 @@ process Subsample {
     shell = ['/bin/bash', '-euo', 'pipefail']
 
     input:
-        tuple(sample_id, val(faction), path(bam_file), path(bai_file))
+        tuple(sample_id, val(fraction), path(bam_file), path(bai_file))
 
     output:
         tuple(sample_id, path("${bam_file.baseName}.subsample.bam"), path("${bam_file.baseName}.subsample.bam.bai"), emit: subsample_bam_file)
 
     script:
         """
-        sambamba view -t ${task.cpus} -f bam -s ${faction} ${params.optional} ${bam_file} -o ${bam_file.baseName}.subsample.bam
+        sambamba view -t ${task.cpus} -f bam -s ${fraction} ${params.optional} ${bam_file} -o ${bam_file.baseName}.subsample.bam
         """
 }

From 5bf79dd2b5f901765a33ce6e1d5c1ddb7803234f Mon Sep 17 00:00:00 2001
From: melferink <m.elferink@umcutrecht.nl>
Date: Thu, 11 May 2023 15:08:03 +0200
Subject: [PATCH 6/7] added new emit options next to summary file

---
 Mosdepth/0.3.3/Mosdepth.nf | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/Mosdepth/0.3.3/Mosdepth.nf b/Mosdepth/0.3.3/Mosdepth.nf
index 4f2aa056..78efea6f 100644
--- a/Mosdepth/0.3.3/Mosdepth.nf
+++ b/Mosdepth/0.3.3/Mosdepth.nf
@@ -8,7 +8,9 @@ process Mosdepth {
         tuple(val(sample_id), path(bam_file), path(bai_file))
 
     output:
-        tuple(sample_id, path("${sample_id}.mosdepth.summary.txt"))
+        tuple(val(sample_id), path("${sample_id}.mosdepth.summary.txt"), emit: summary_file)
+        tuple(val(sample_id), path("${sample_id}.mosdepth.*.txt"), emit: txt_files)
+        tuple(val(sample_id), path("${sample_id}*bed*"), emit: bed_files, optional: true)
 
     script:
         """

From b6bf5acb71acbf985a2614efbadd8f1aba34921d Mon Sep 17 00:00:00 2001
From: melferink <m.elferink@umcutrecht.nl>
Date: Mon, 15 May 2023 13:13:29 +0200
Subject: [PATCH 7/7] renamed for consistency

---
 Sambamba/0.7.0/ViewSubsample.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Sambamba/0.7.0/ViewSubsample.nf b/Sambamba/0.7.0/ViewSubsample.nf
index 88ddf5ad..b109d219 100644
--- a/Sambamba/0.7.0/ViewSubsample.nf
+++ b/Sambamba/0.7.0/ViewSubsample.nf
@@ -9,7 +9,7 @@ process Subsample {
         tuple(sample_id, val(fraction), path(bam_file), path(bai_file))
 
     output:
-        tuple(sample_id, path("${bam_file.baseName}.subsample.bam"), path("${bam_file.baseName}.subsample.bam.bai"), emit: subsample_bam_file)
+        tuple(sample_id, path("${bam_file.baseName}.subsample.bam"), path("${bam_file.baseName}.subsample.bam.bai"), emit: bam_file)
 
     script:
         """