From 30128fc03a631571b16d935e88eacd02b98231d5 Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Tue, 30 Apr 2024 13:30:05 +0200
Subject: [PATCH 01/23] ignore error from bwa-mem2 and if output is missing,
 run bwa

---
 conf/modules/align_bwa_bwamem2.config             |  1 +
 subworkflows/local/alignment/align_bwa_bwamem2.nf | 10 +++++-----
 2 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/conf/modules/align_bwa_bwamem2.config b/conf/modules/align_bwa_bwamem2.config
index e91360fc..d82fb5d6 100644
--- a/conf/modules/align_bwa_bwamem2.config
+++ b/conf/modules/align_bwa_bwamem2.config
@@ -23,6 +23,7 @@ process {
             ext.args = { "-M -K 100000000 -R ${meta.read_group}" }
             ext.prefix = { "${meta.id}_sorted" }
             ext.when = { params.aligner.equals("bwamem2") }
+            label = 'error_ignore'
         }
 
         withName: '.*ALIGN:ALIGN_BWA_BWAMEM2:BWA_MEM' {
diff --git a/subworkflows/local/alignment/align_bwa_bwamem2.nf b/subworkflows/local/alignment/align_bwa_bwamem2.nf
index 10537898..6d5847a7 100644
--- a/subworkflows/local/alignment/align_bwa_bwamem2.nf
+++ b/subworkflows/local/alignment/align_bwa_bwamem2.nf
@@ -24,14 +24,14 @@ workflow ALIGN_BWA_BWAMEM2 {
         ch_versions = Channel.empty()
 
         // Map, sort, and index
-        if (params.aligner.equals("bwa")) {
-            BWA_MEM ( ch_reads_input, ch_bwa_index, true )
-            ch_align = BWA_MEM.out.bam
-            ch_versions = ch_versions.mix(BWA_MEM.out.versions.first())
-        } else {
+        if (params.aligner.equals("bwamem2")) {
             BWAMEM2_MEM ( ch_reads_input, ch_bwamem2_index, true )
             ch_align = BWAMEM2_MEM.out.bam
             ch_versions = ch_versions.mix(BWAMEM2_MEM.out.versions.first())
+        else if (params.aligner.equals("bwa") || !BWAMEM2_MEM.out.bam.exists()) {
+            BWA_MEM ( ch_reads_input, ch_bwa_index, true )
+            ch_align = BWA_MEM.out.bam
+            ch_versions = ch_versions.mix(BWA_MEM.out.versions.first())
         }
 
         SAMTOOLS_INDEX_ALIGN ( ch_align )

From 5accab2506ea70661860f038631c0dedfc9f781f Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Tue, 30 Apr 2024 13:30:41 +0200
Subject: [PATCH 02/23] change logical gate

---
 subworkflows/local/alignment/align_bwa_bwamem2.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/subworkflows/local/alignment/align_bwa_bwamem2.nf b/subworkflows/local/alignment/align_bwa_bwamem2.nf
index 6d5847a7..650c5fc6 100644
--- a/subworkflows/local/alignment/align_bwa_bwamem2.nf
+++ b/subworkflows/local/alignment/align_bwa_bwamem2.nf
@@ -28,7 +28,7 @@ workflow ALIGN_BWA_BWAMEM2 {
             BWAMEM2_MEM ( ch_reads_input, ch_bwamem2_index, true )
             ch_align = BWAMEM2_MEM.out.bam
             ch_versions = ch_versions.mix(BWAMEM2_MEM.out.versions.first())
-        else if (params.aligner.equals("bwa") || !BWAMEM2_MEM.out.bam.exists()) {
+        else if (params.aligner.equals("bwa") || (params.aligner.equals("bwamem2") && !BWAMEM2_MEM.out.bam.exists())) {
             BWA_MEM ( ch_reads_input, ch_bwa_index, true )
             ch_align = BWA_MEM.out.bam
             ch_versions = ch_versions.mix(BWA_MEM.out.versions.first())

From afeefc1a5c221ff174571d4878db92aea3e97e56 Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Tue, 30 Apr 2024 13:36:47 +0200
Subject: [PATCH 03/23] typo

---
 subworkflows/local/alignment/align_bwa_bwamem2.nf | 1 +
 1 file changed, 1 insertion(+)

diff --git a/subworkflows/local/alignment/align_bwa_bwamem2.nf b/subworkflows/local/alignment/align_bwa_bwamem2.nf
index 650c5fc6..e26d4bde 100644
--- a/subworkflows/local/alignment/align_bwa_bwamem2.nf
+++ b/subworkflows/local/alignment/align_bwa_bwamem2.nf
@@ -28,6 +28,7 @@ workflow ALIGN_BWA_BWAMEM2 {
             BWAMEM2_MEM ( ch_reads_input, ch_bwamem2_index, true )
             ch_align = BWAMEM2_MEM.out.bam
             ch_versions = ch_versions.mix(BWAMEM2_MEM.out.versions.first())
+        }
         else if (params.aligner.equals("bwa") || (params.aligner.equals("bwamem2") && !BWAMEM2_MEM.out.bam.exists())) {
             BWA_MEM ( ch_reads_input, ch_bwa_index, true )
             ch_align = BWA_MEM.out.bam

From 2d2efd2382de6698786686b3572897b1a3e322fd Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Tue, 30 Apr 2024 13:49:25 +0200
Subject: [PATCH 04/23] change syntax

---
 conf/modules/align_bwa_bwamem2.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/conf/modules/align_bwa_bwamem2.config b/conf/modules/align_bwa_bwamem2.config
index d82fb5d6..cf5e79f8 100644
--- a/conf/modules/align_bwa_bwamem2.config
+++ b/conf/modules/align_bwa_bwamem2.config
@@ -23,7 +23,7 @@ process {
             ext.args = { "-M -K 100000000 -R ${meta.read_group}" }
             ext.prefix = { "${meta.id}_sorted" }
             ext.when = { params.aligner.equals("bwamem2") }
-            label = 'error_ignore'
+            errorStrategy = 'ignore'
         }
 
         withName: '.*ALIGN:ALIGN_BWA_BWAMEM2:BWA_MEM' {

From 52b7caa8411216e3f04e9633a2871851cea504c0 Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Tue, 30 Apr 2024 13:53:37 +0200
Subject: [PATCH 05/23] change logical gate

---
 subworkflows/local/alignment/align_bwa_bwamem2.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/subworkflows/local/alignment/align_bwa_bwamem2.nf b/subworkflows/local/alignment/align_bwa_bwamem2.nf
index e26d4bde..6ee8dfc9 100644
--- a/subworkflows/local/alignment/align_bwa_bwamem2.nf
+++ b/subworkflows/local/alignment/align_bwa_bwamem2.nf
@@ -29,7 +29,7 @@ workflow ALIGN_BWA_BWAMEM2 {
             ch_align = BWAMEM2_MEM.out.bam
             ch_versions = ch_versions.mix(BWAMEM2_MEM.out.versions.first())
         }
-        else if (params.aligner.equals("bwa") || (params.aligner.equals("bwamem2") && !BWAMEM2_MEM.out.bam.exists())) {
+        if (params.aligner.equals("bwa") || (params.aligner.equals("bwamem2") && !BWAMEM2_MEM.out.bam.exists())) {
             BWA_MEM ( ch_reads_input, ch_bwa_index, true )
             ch_align = BWA_MEM.out.bam
             ch_versions = ch_versions.mix(BWA_MEM.out.versions.first())

From 2c0bdb028434045076490960bc51c7ee53ec9dd1 Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Tue, 30 Apr 2024 14:24:45 +0200
Subject: [PATCH 06/23] change logical gate

---
 subworkflows/local/alignment/align_bwa_bwamem2.nf | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/subworkflows/local/alignment/align_bwa_bwamem2.nf b/subworkflows/local/alignment/align_bwa_bwamem2.nf
index 6ee8dfc9..acf684e0 100644
--- a/subworkflows/local/alignment/align_bwa_bwamem2.nf
+++ b/subworkflows/local/alignment/align_bwa_bwamem2.nf
@@ -22,14 +22,15 @@ workflow ALIGN_BWA_BWAMEM2 {
 
     main:
         ch_versions = Channel.empty()
-
+        count = 0
         // Map, sort, and index
         if (params.aligner.equals("bwamem2")) {
             BWAMEM2_MEM ( ch_reads_input, ch_bwamem2_index, true )
             ch_align = BWAMEM2_MEM.out.bam
             ch_versions = ch_versions.mix(BWAMEM2_MEM.out.versions.first())
+            count = BWAMEM2_MEM.out.bam.ifEmpty(1)
         }
-        if (params.aligner.equals("bwa") || (params.aligner.equals("bwamem2") && !BWAMEM2_MEM.out.bam.exists())) {
+        if (params.aligner.equals("bwa") || count == 1) {
             BWA_MEM ( ch_reads_input, ch_bwa_index, true )
             ch_align = BWA_MEM.out.bam
             ch_versions = ch_versions.mix(BWA_MEM.out.versions.first())

From ecd62865665c2026f85587607f9661726017ba02 Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Thu, 2 May 2024 11:38:53 +0200
Subject: [PATCH 07/23] try a retry with more memory

---
 conf/modules/align_bwa_bwamem2.config             |  2 +-
 subworkflows/local/alignment/align_bwa_bwamem2.nf | 14 ++++++--------
 2 files changed, 7 insertions(+), 9 deletions(-)

diff --git a/conf/modules/align_bwa_bwamem2.config b/conf/modules/align_bwa_bwamem2.config
index cf5e79f8..ff53af13 100644
--- a/conf/modules/align_bwa_bwamem2.config
+++ b/conf/modules/align_bwa_bwamem2.config
@@ -23,7 +23,7 @@ process {
             ext.args = { "-M -K 100000000 -R ${meta.read_group}" }
             ext.prefix = { "${meta.id}_sorted" }
             ext.when = { params.aligner.equals("bwamem2") }
-            errorStrategy = 'ignore'
+            errorStrategy = { task.exitStatus in (1 + (130..145) + 104) ? 'retry' : 'finish' }
         }
 
         withName: '.*ALIGN:ALIGN_BWA_BWAMEM2:BWA_MEM' {
diff --git a/subworkflows/local/alignment/align_bwa_bwamem2.nf b/subworkflows/local/alignment/align_bwa_bwamem2.nf
index acf684e0..10537898 100644
--- a/subworkflows/local/alignment/align_bwa_bwamem2.nf
+++ b/subworkflows/local/alignment/align_bwa_bwamem2.nf
@@ -22,18 +22,16 @@ workflow ALIGN_BWA_BWAMEM2 {
 
     main:
         ch_versions = Channel.empty()
-        count = 0
+
         // Map, sort, and index
-        if (params.aligner.equals("bwamem2")) {
-            BWAMEM2_MEM ( ch_reads_input, ch_bwamem2_index, true )
-            ch_align = BWAMEM2_MEM.out.bam
-            ch_versions = ch_versions.mix(BWAMEM2_MEM.out.versions.first())
-            count = BWAMEM2_MEM.out.bam.ifEmpty(1)
-        }
-        if (params.aligner.equals("bwa") || count == 1) {
+        if (params.aligner.equals("bwa")) {
             BWA_MEM ( ch_reads_input, ch_bwa_index, true )
             ch_align = BWA_MEM.out.bam
             ch_versions = ch_versions.mix(BWA_MEM.out.versions.first())
+        } else {
+            BWAMEM2_MEM ( ch_reads_input, ch_bwamem2_index, true )
+            ch_align = BWAMEM2_MEM.out.bam
+            ch_versions = ch_versions.mix(BWAMEM2_MEM.out.versions.first())
         }
 
         SAMTOOLS_INDEX_ALIGN ( ch_align )

From eee78184da59049ce512d1308aebf28a0ba8d2d3 Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Thu, 2 May 2024 13:50:05 +0200
Subject: [PATCH 08/23] try a retry with more memory

---
 conf/modules/align_bwa_bwamem2.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/conf/modules/align_bwa_bwamem2.config b/conf/modules/align_bwa_bwamem2.config
index ff53af13..04739e9a 100644
--- a/conf/modules/align_bwa_bwamem2.config
+++ b/conf/modules/align_bwa_bwamem2.config
@@ -23,7 +23,7 @@ process {
             ext.args = { "-M -K 100000000 -R ${meta.read_group}" }
             ext.prefix = { "${meta.id}_sorted" }
             ext.when = { params.aligner.equals("bwamem2") }
-            errorStrategy = { task.exitStatus in (1 + (130..145) + 104) ? 'retry' : 'finish' }
+            errorStrategy = { task.exitStatus in (1, (130..145), 104) ? 'retry' : 'finish' }
         }
 
         withName: '.*ALIGN:ALIGN_BWA_BWAMEM2:BWA_MEM' {

From 85fc2ea7fbcac4848899852ff81b3b9661b6dc28 Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Thu, 2 May 2024 14:22:21 +0200
Subject: [PATCH 09/23] try a retry with more memory

---
 conf/modules/align_bwa_bwamem2.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/conf/modules/align_bwa_bwamem2.config b/conf/modules/align_bwa_bwamem2.config
index 04739e9a..30d961e7 100644
--- a/conf/modules/align_bwa_bwamem2.config
+++ b/conf/modules/align_bwa_bwamem2.config
@@ -23,7 +23,7 @@ process {
             ext.args = { "-M -K 100000000 -R ${meta.read_group}" }
             ext.prefix = { "${meta.id}_sorted" }
             ext.when = { params.aligner.equals("bwamem2") }
-            errorStrategy = { task.exitStatus in (1, (130..145), 104) ? 'retry' : 'finish' }
+            errorStrategy = { task.exitStatus in [1,104,130,131,132,133,134,135,135,136,137,138,139,140,141,142,143,144,145] ? 'retry' : 'finish' }
         }
 
         withName: '.*ALIGN:ALIGN_BWA_BWAMEM2:BWA_MEM' {

From f6d99dcb548e8e4679842c4d0c862c57bbc2f4be Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Thu, 2 May 2024 16:32:11 +0200
Subject: [PATCH 10/23] change logic

---
 conf/modules/align_bwa_bwamem2.config           |  2 +-
 .../local/alignment/align_bwa_bwamem2.nf        | 17 +++++++++++------
 2 files changed, 12 insertions(+), 7 deletions(-)

diff --git a/conf/modules/align_bwa_bwamem2.config b/conf/modules/align_bwa_bwamem2.config
index 30d961e7..cf5e79f8 100644
--- a/conf/modules/align_bwa_bwamem2.config
+++ b/conf/modules/align_bwa_bwamem2.config
@@ -23,7 +23,7 @@ process {
             ext.args = { "-M -K 100000000 -R ${meta.read_group}" }
             ext.prefix = { "${meta.id}_sorted" }
             ext.when = { params.aligner.equals("bwamem2") }
-            errorStrategy = { task.exitStatus in [1,104,130,131,132,133,134,135,135,136,137,138,139,140,141,142,143,144,145] ? 'retry' : 'finish' }
+            errorStrategy = 'ignore'
         }
 
         withName: '.*ALIGN:ALIGN_BWA_BWAMEM2:BWA_MEM' {
diff --git a/subworkflows/local/alignment/align_bwa_bwamem2.nf b/subworkflows/local/alignment/align_bwa_bwamem2.nf
index 10537898..3499551e 100644
--- a/subworkflows/local/alignment/align_bwa_bwamem2.nf
+++ b/subworkflows/local/alignment/align_bwa_bwamem2.nf
@@ -24,14 +24,19 @@ workflow ALIGN_BWA_BWAMEM2 {
         ch_versions = Channel.empty()
 
         // Map, sort, and index
-        if (params.aligner.equals("bwa")) {
-            BWA_MEM ( ch_reads_input, ch_bwa_index, true )
-            ch_align = BWA_MEM.out.bam
-            ch_versions = ch_versions.mix(BWA_MEM.out.versions.first())
-        } else {
+        if (params.aligner.equals("bwamem2")) {
             BWAMEM2_MEM ( ch_reads_input, ch_bwamem2_index, true )
-            ch_align = BWAMEM2_MEM.out.bam
             ch_versions = ch_versions.mix(BWAMEM2_MEM.out.versions.first())
+
+
+            if  (BWA_MEM.out.bam.ifEmpty()) {
+                BWA_MEM ( ch_reads_input, ch_bwa_index, true )
+                ch_versions = ch_versions.mix(BWA_MEM.out.versions.first())
+                ch_align = BWA_MEM.out.bam
+
+            else {
+                ch_align = BWAMEM2_MEM.out.bam
+            }
         }
 
         SAMTOOLS_INDEX_ALIGN ( ch_align )

From 17ed5d4900efc57fa0b0c4ad9d183c15056f1130 Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Thu, 2 May 2024 16:44:17 +0200
Subject: [PATCH 11/23] change logic

---
 subworkflows/local/alignment/align_bwa_bwamem2.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/subworkflows/local/alignment/align_bwa_bwamem2.nf b/subworkflows/local/alignment/align_bwa_bwamem2.nf
index 3499551e..62fb99df 100644
--- a/subworkflows/local/alignment/align_bwa_bwamem2.nf
+++ b/subworkflows/local/alignment/align_bwa_bwamem2.nf
@@ -29,11 +29,11 @@ workflow ALIGN_BWA_BWAMEM2 {
             ch_versions = ch_versions.mix(BWAMEM2_MEM.out.versions.first())
 
 
-            if  (BWA_MEM.out.bam.ifEmpty()) {
+            if  (BWAMEM2_MEM.out.bam.ifEmpty()) {
                 BWA_MEM ( ch_reads_input, ch_bwa_index, true )
                 ch_versions = ch_versions.mix(BWA_MEM.out.versions.first())
                 ch_align = BWA_MEM.out.bam
-
+            }
             else {
                 ch_align = BWAMEM2_MEM.out.bam
             }

From 8adc86f77838dae0ed6580e85f3a87e9791f88aa Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Thu, 2 May 2024 17:00:33 +0200
Subject: [PATCH 12/23] change logic

---
 subworkflows/local/alignment/align_bwa_bwamem2.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/subworkflows/local/alignment/align_bwa_bwamem2.nf b/subworkflows/local/alignment/align_bwa_bwamem2.nf
index 62fb99df..8c7a189a 100644
--- a/subworkflows/local/alignment/align_bwa_bwamem2.nf
+++ b/subworkflows/local/alignment/align_bwa_bwamem2.nf
@@ -29,7 +29,7 @@ workflow ALIGN_BWA_BWAMEM2 {
             ch_versions = ch_versions.mix(BWAMEM2_MEM.out.versions.first())
 
 
-            if  (BWAMEM2_MEM.out.bam.ifEmpty()) {
+            if  (BWAMEM2_MEM.out.bam.ifEmpty(False)) {
                 BWA_MEM ( ch_reads_input, ch_bwa_index, true )
                 ch_versions = ch_versions.mix(BWA_MEM.out.versions.first())
                 ch_align = BWA_MEM.out.bam

From ad00cbc9474d2479c3c28f85ceb8a18bf5214847 Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Fri, 3 May 2024 11:01:05 +0200
Subject: [PATCH 13/23] change if statement

---
 subworkflows/local/alignment/align_bwa_bwamem2.nf | 14 +++++++++-----
 1 file changed, 9 insertions(+), 5 deletions(-)

diff --git a/subworkflows/local/alignment/align_bwa_bwamem2.nf b/subworkflows/local/alignment/align_bwa_bwamem2.nf
index 8c7a189a..79ca1640 100644
--- a/subworkflows/local/alignment/align_bwa_bwamem2.nf
+++ b/subworkflows/local/alignment/align_bwa_bwamem2.nf
@@ -22,22 +22,26 @@ workflow ALIGN_BWA_BWAMEM2 {
 
     main:
         ch_versions = Channel.empty()
+        ch_align = Channel.empty()
 
         // Map, sort, and index
         if (params.aligner.equals("bwamem2")) {
             BWAMEM2_MEM ( ch_reads_input, ch_bwamem2_index, true )
             ch_versions = ch_versions.mix(BWAMEM2_MEM.out.versions.first())
+            ch_align = BWAMEM2_MEM.out.bam
 
-
-            if  (BWAMEM2_MEM.out.bam.ifEmpty(False)) {
+            if  (ch_align == Channel.empty) {
                 BWA_MEM ( ch_reads_input, ch_bwa_index, true )
                 ch_versions = ch_versions.mix(BWA_MEM.out.versions.first())
                 ch_align = BWA_MEM.out.bam
             }
-            else {
-                ch_align = BWAMEM2_MEM.out.bam
-            }
         }
+        else if (params.aligner.equals("bwamem2"){
+                BWA_MEM ( ch_reads_input, ch_bwa_index, true )
+                ch_versions = ch_versions.mix(BWA_MEM.out.versions.first())
+                ch_align = BWA_MEM.out.bam
+            }
+
 
         SAMTOOLS_INDEX_ALIGN ( ch_align )
 

From 7ba937f31556c80f6908270bcd3136829b78277a Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Fri, 3 May 2024 11:09:58 +0200
Subject: [PATCH 14/23] change if statement

---
 subworkflows/local/alignment/align_bwa_bwamem2.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/subworkflows/local/alignment/align_bwa_bwamem2.nf b/subworkflows/local/alignment/align_bwa_bwamem2.nf
index 79ca1640..78c4974c 100644
--- a/subworkflows/local/alignment/align_bwa_bwamem2.nf
+++ b/subworkflows/local/alignment/align_bwa_bwamem2.nf
@@ -30,13 +30,13 @@ workflow ALIGN_BWA_BWAMEM2 {
             ch_versions = ch_versions.mix(BWAMEM2_MEM.out.versions.first())
             ch_align = BWAMEM2_MEM.out.bam
 
-            if  (ch_align == Channel.empty) {
+            if  (ch_align == Channel.empty()) {
                 BWA_MEM ( ch_reads_input, ch_bwa_index, true )
                 ch_versions = ch_versions.mix(BWA_MEM.out.versions.first())
                 ch_align = BWA_MEM.out.bam
             }
         }
-        else if (params.aligner.equals("bwamem2"){
+        else if (params.aligner.equals("bwa")){
                 BWA_MEM ( ch_reads_input, ch_bwa_index, true )
                 ch_versions = ch_versions.mix(BWA_MEM.out.versions.first())
                 ch_align = BWA_MEM.out.bam

From b2c0eb1855f99060d252e4cc53fc0796e50a5288 Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Fri, 3 May 2024 11:37:14 +0200
Subject: [PATCH 15/23] change if statement

---
 subworkflows/local/alignment/align_bwa_bwamem2.nf | 13 ++++---------
 1 file changed, 4 insertions(+), 9 deletions(-)

diff --git a/subworkflows/local/alignment/align_bwa_bwamem2.nf b/subworkflows/local/alignment/align_bwa_bwamem2.nf
index 78c4974c..acc1546e 100644
--- a/subworkflows/local/alignment/align_bwa_bwamem2.nf
+++ b/subworkflows/local/alignment/align_bwa_bwamem2.nf
@@ -22,26 +22,21 @@ workflow ALIGN_BWA_BWAMEM2 {
 
     main:
         ch_versions = Channel.empty()
-        ch_align = Channel.empty()
 
         // Map, sort, and index
         if (params.aligner.equals("bwamem2")) {
             BWAMEM2_MEM ( ch_reads_input, ch_bwamem2_index, true )
             ch_versions = ch_versions.mix(BWAMEM2_MEM.out.versions.first())
-            ch_align = BWAMEM2_MEM.out.bam
 
-            if  (ch_align == Channel.empty()) {
+            if  (!file.exists(BWAMEM2_MEM.out.bam)) {
                 BWA_MEM ( ch_reads_input, ch_bwa_index, true )
                 ch_versions = ch_versions.mix(BWA_MEM.out.versions.first())
                 ch_align = BWA_MEM.out.bam
             }
-        }
-        else if (params.aligner.equals("bwa")){
-                BWA_MEM ( ch_reads_input, ch_bwa_index, true )
-                ch_versions = ch_versions.mix(BWA_MEM.out.versions.first())
-                ch_align = BWA_MEM.out.bam
+            else {
+                ch_align = BWAMEM2_MEM.out.bam
             }
-
+        }
 
         SAMTOOLS_INDEX_ALIGN ( ch_align )
 

From 98e202a017058d041a501186068d412ea385f088 Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Fri, 3 May 2024 12:10:25 +0200
Subject: [PATCH 16/23] change if statement

---
 subworkflows/local/alignment/align_bwa_bwamem2.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/subworkflows/local/alignment/align_bwa_bwamem2.nf b/subworkflows/local/alignment/align_bwa_bwamem2.nf
index acc1546e..0871b063 100644
--- a/subworkflows/local/alignment/align_bwa_bwamem2.nf
+++ b/subworkflows/local/alignment/align_bwa_bwamem2.nf
@@ -28,7 +28,7 @@ workflow ALIGN_BWA_BWAMEM2 {
             BWAMEM2_MEM ( ch_reads_input, ch_bwamem2_index, true )
             ch_versions = ch_versions.mix(BWAMEM2_MEM.out.versions.first())
 
-            if  (!file.exists(BWAMEM2_MEM.out.bam)) {
+            if  (!(BWAMEM2_MEM.out.bam).exists()) {
                 BWA_MEM ( ch_reads_input, ch_bwa_index, true )
                 ch_versions = ch_versions.mix(BWA_MEM.out.versions.first())
                 ch_align = BWA_MEM.out.bam

From e811efd82a5523ff38fe53d4b487bb5292504af1 Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Fri, 3 May 2024 12:53:41 +0200
Subject: [PATCH 17/23] change if statement

---
 subworkflows/local/alignment/align_bwa_bwamem2.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/subworkflows/local/alignment/align_bwa_bwamem2.nf b/subworkflows/local/alignment/align_bwa_bwamem2.nf
index 0871b063..730a95e4 100644
--- a/subworkflows/local/alignment/align_bwa_bwamem2.nf
+++ b/subworkflows/local/alignment/align_bwa_bwamem2.nf
@@ -28,7 +28,7 @@ workflow ALIGN_BWA_BWAMEM2 {
             BWAMEM2_MEM ( ch_reads_input, ch_bwamem2_index, true )
             ch_versions = ch_versions.mix(BWAMEM2_MEM.out.versions.first())
 
-            if  (!(BWAMEM2_MEM.out.bam).exists()) {
+            if  ((BWAMEM2_MEM.out.bam).isEmpty()) {
                 BWA_MEM ( ch_reads_input, ch_bwa_index, true )
                 ch_versions = ch_versions.mix(BWA_MEM.out.versions.first())
                 ch_align = BWA_MEM.out.bam

From 68f9bc892d7cc46c6f4fa1546891f2ba6b34631a Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Fri, 3 May 2024 14:31:29 +0200
Subject: [PATCH 18/23] add tmp channel

---
 subworkflows/local/alignment/align_bwa_bwamem2.nf | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/subworkflows/local/alignment/align_bwa_bwamem2.nf b/subworkflows/local/alignment/align_bwa_bwamem2.nf
index 730a95e4..f7e5cb19 100644
--- a/subworkflows/local/alignment/align_bwa_bwamem2.nf
+++ b/subworkflows/local/alignment/align_bwa_bwamem2.nf
@@ -22,13 +22,13 @@ workflow ALIGN_BWA_BWAMEM2 {
 
     main:
         ch_versions = Channel.empty()
-
+        ch_align_tmp = Channel.empty()
         // Map, sort, and index
         if (params.aligner.equals("bwamem2")) {
             BWAMEM2_MEM ( ch_reads_input, ch_bwamem2_index, true )
             ch_versions = ch_versions.mix(BWAMEM2_MEM.out.versions.first())
-
-            if  ((BWAMEM2_MEM.out.bam).isEmpty()) {
+            ch_align_tmp = BWAMEM2_MEM.out.bam
+            if  (!ch_align_tmp) {
                 BWA_MEM ( ch_reads_input, ch_bwa_index, true )
                 ch_versions = ch_versions.mix(BWA_MEM.out.versions.first())
                 ch_align = BWA_MEM.out.bam

From e6b62b7a9504f4db4bd1af7bc38a7d852790a122 Mon Sep 17 00:00:00 2001
From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Date: Mon, 6 May 2024 16:09:41 +0200
Subject: [PATCH 19/23] update align

---
 .../local/alignment/align_bwa_bwamem2.nf      | 34 +++++++++++++------
 1 file changed, 24 insertions(+), 10 deletions(-)

diff --git a/subworkflows/local/alignment/align_bwa_bwamem2.nf b/subworkflows/local/alignment/align_bwa_bwamem2.nf
index f7e5cb19..16fff1bc 100644
--- a/subworkflows/local/alignment/align_bwa_bwamem2.nf
+++ b/subworkflows/local/alignment/align_bwa_bwamem2.nf
@@ -3,6 +3,7 @@
 //
 
 include { BWA_MEM                                  } from '../../../modules/nf-core/bwa/mem/main'
+include { BWA_MEM as BWAMEM_FALLBACK               } from '../../../modules/nf-core/bwa/mem/main'
 include { BWAMEM2_MEM                              } from '../../../modules/nf-core/bwamem2/mem/main'
 include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_ALIGN   } from '../../../modules/nf-core/samtools/index/main'
 include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_MARKDUP } from '../../../modules/nf-core/samtools/index/main'
@@ -22,20 +23,33 @@ workflow ALIGN_BWA_BWAMEM2 {
 
     main:
         ch_versions = Channel.empty()
-        ch_align_tmp = Channel.empty()
+
         // Map, sort, and index
-        if (params.aligner.equals("bwamem2")) {
+        if (params.aligner.equals("bwa")) {
+            BWA_MEM ( ch_reads_input, ch_bwa_index, true )
+            ch_align = BWA_MEM.out.bam
+            ch_versions = ch_versions.mix(BWA_MEM.out.versions.first())
+        } else {
             BWAMEM2_MEM ( ch_reads_input, ch_bwamem2_index, true )
+            ch_align    = BWAMEM2_MEM.out.bam
             ch_versions = ch_versions.mix(BWAMEM2_MEM.out.versions.first())
-            ch_align_tmp = BWAMEM2_MEM.out.bam
-            if  (!ch_align_tmp) {
-                BWA_MEM ( ch_reads_input, ch_bwa_index, true )
-                ch_versions = ch_versions.mix(BWA_MEM.out.versions.first())
-                ch_align = BWA_MEM.out.bam
-            }
-            else {
-                ch_align = BWAMEM2_MEM.out.bam
+
+            if (params.align_fallback.equals(true)) {
+                ch_reads_input
+                    .join(BWAMEM2_MEM.out.bam, remainder: true)
+                    .branch { it ->
+                        ERROR: it[2].equals(null)
+                            return [it[0], it[1]] // return reads
+                        SUCCESS: !it[2].equals(null)
+                            return [it[0], it[2]]  // return bam
+                    }
+                    .set { ch_fallback }
+
+                BWAMEM_FALLBACK ( ch_fallback.ERROR, ch_bwa_index, true )
+                ch_align = ch_fallback.SUCCESS.mix(BWAMEM_FALLBACK.out.bam)
+                ch_versions = ch_versions.mix(BWAMEM_FALLBACK.out.versions.first())
             }
+
         }
 
         SAMTOOLS_INDEX_ALIGN ( ch_align )

From cad7ce23becf08d7033f5621927f5bc4046a6eac Mon Sep 17 00:00:00 2001
From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Date: Tue, 7 May 2024 10:40:32 +0200
Subject: [PATCH 20/23] update param

---
 nextflow.config                                   | 1 +
 nextflow_schema.json                              | 5 +++++
 subworkflows/local/alignment/align_bwa_bwamem2.nf | 2 +-
 3 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/nextflow.config b/nextflow.config
index 5065d2d9..fb385fa6 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -22,6 +22,7 @@ params {
 
     // Main options
     analysis_type              = 'wgs'
+    bwa_as_fallback            = false
     bait_padding               = 100
     run_rtgvcfeval             = false
     save_mapped_as_cram        = false
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 6e2fbc81..1d1049bd 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -459,6 +459,11 @@
             "fa_icon": "fas fa-user-cog",
             "description": "Options used to steer the direction of the pipeline.",
             "properties": {
+                "bwa_as_fallback": {
+                    "type": "boolean",
+                    "description": "Specifies whether or not to use bwa as a fallback aligner in case bwamem2 throws an error.",
+                    "fa_icon": "fas fa-toggle-on"
+                },
                 "analysis_type": {
                     "type": "string",
                     "default": "wgs",
diff --git a/subworkflows/local/alignment/align_bwa_bwamem2.nf b/subworkflows/local/alignment/align_bwa_bwamem2.nf
index 80bf3822..40e93196 100644
--- a/subworkflows/local/alignment/align_bwa_bwamem2.nf
+++ b/subworkflows/local/alignment/align_bwa_bwamem2.nf
@@ -34,7 +34,7 @@ workflow ALIGN_BWA_BWAMEM2 {
             ch_align    = BWAMEM2_MEM.out.bam
             ch_versions = ch_versions.mix(BWAMEM2_MEM.out.versions.first())
 
-            if (params.align_fallback.equals(true)) {
+            if (params.bwa_as_fallback.equals(true)) {
                 ch_reads_input
                     .join(BWAMEM2_MEM.out.bam, remainder: true)
                     .branch { it ->

From 7efe3b876169a97e9c03eb214efe703cdbd01e8a Mon Sep 17 00:00:00 2001
From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Date: Tue, 7 May 2024 15:04:19 +0200
Subject: [PATCH 21/23] arrange param

---
 nextflow_schema.json | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/nextflow_schema.json b/nextflow_schema.json
index 1d1049bd..d70f69ed 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -459,11 +459,6 @@
             "fa_icon": "fas fa-user-cog",
             "description": "Options used to steer the direction of the pipeline.",
             "properties": {
-                "bwa_as_fallback": {
-                    "type": "boolean",
-                    "description": "Specifies whether or not to use bwa as a fallback aligner in case bwamem2 throws an error.",
-                    "fa_icon": "fas fa-toggle-on"
-                },
                 "analysis_type": {
                     "type": "string",
                     "default": "wgs",
@@ -471,6 +466,11 @@
                     "fa_icon": "fas fa-align-center",
                     "enum": ["wgs", "wes", "mito"]
                 },
+                "bwa_as_fallback": {
+                    "type": "boolean",
+                    "description": "Specifies whether or not to use bwa as a fallback aligner in case bwamem2 throws an error.",
+                    "fa_icon": "fas fa-toggle-on"
+                },
                 "platform": {
                     "type": "string",
                     "default": "illumina",

From 91fc58e3a39ab8ff37eb9154f5ee48f155bef579 Mon Sep 17 00:00:00 2001
From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Date: Fri, 17 May 2024 13:14:52 +0200
Subject: [PATCH 22/23] update changelog

---
 CHANGELOG.md         | 2 ++
 nextflow_schema.json | 1 +
 2 files changed, 3 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 2e74f569..44e6f516 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,6 +7,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Added`
 
+- A new parameter `bwa_as_fallback` to switch aligner to bwa in case bwamem2 fails [#551](https://github.com/nf-core/raredisease/pull/551)
+
 ### `Changed`
 
 - Refactored config files [#538](https://github.com/nf-core/raredisease/pull/538)
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 0c26050c..674c19c8 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -468,6 +468,7 @@
                 "bwa_as_fallback": {
                     "type": "boolean",
                     "description": "Specifies whether or not to use bwa as a fallback aligner in case bwamem2 throws an error.",
+                    "help_text": "errorStrategy needs to be set to ignore for the bwamem2 process for the fallback to work. Turned off by default.",
                     "fa_icon": "fas fa-toggle-on"
                 },
                 "platform": {

From 2d5c9181d1cd8900b26bab78b37cd28151a85ee9 Mon Sep 17 00:00:00 2001
From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Date: Fri, 17 May 2024 22:19:00 +0200
Subject: [PATCH 23/23] Update align_bwa_bwamem2.nf

---
 subworkflows/local/alignment/align_bwa_bwamem2.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/subworkflows/local/alignment/align_bwa_bwamem2.nf b/subworkflows/local/alignment/align_bwa_bwamem2.nf
index 40e93196..b846cad3 100644
--- a/subworkflows/local/alignment/align_bwa_bwamem2.nf
+++ b/subworkflows/local/alignment/align_bwa_bwamem2.nf
@@ -34,7 +34,7 @@ workflow ALIGN_BWA_BWAMEM2 {
             ch_align    = BWAMEM2_MEM.out.bam
             ch_versions = ch_versions.mix(BWAMEM2_MEM.out.versions.first())
 
-            if (params.bwa_as_fallback.equals(true)) {
+            if (params.bwa_as_fallback) {
                 ch_reads_input
                     .join(BWAMEM2_MEM.out.bam, remainder: true)
                     .branch { it ->