From 7a9877745c47d69c3f938a56ec97384cf4deab0f Mon Sep 17 00:00:00 2001
From: Marijon Pierre <pierre.marijon@inria.fr>
Date: Sat, 13 Oct 2018 23:55:29 +0200
Subject: [PATCH 1/7] Add bcalm flowcraft

---
 flowcraft/generator/components/assembly.py | 44 ++++++++++++++++++++++
 flowcraft/generator/engine.py              |  1 +
 flowcraft/generator/templates/bcalm.nf     | 30 +++++++++++++++
 3 files changed, 75 insertions(+)
 create mode 100644 flowcraft/generator/templates/bcalm.nf

diff --git a/flowcraft/generator/components/assembly.py b/flowcraft/generator/components/assembly.py
index d6d8f8d4..1073a83e 100644
--- a/flowcraft/generator/components/assembly.py
+++ b/flowcraft/generator/components/assembly.py
@@ -4,6 +4,50 @@
 except ImportError:
     from flowcraft.generator.process import Process
 
+class Bcalm(Process):
+    """Bcalm process template interface
+
+    This process is set with:
+
+        - ``input_type``: fastq
+        - ``output_type``: assembly
+        - ``ptype``: assembly
+
+    """
+
+    def __init__(self, **kwargs):
+
+        super().__init__(**kwargs)
+
+        self.input_type = "fastq"
+        self.output_type = "fasta"
+
+        self.dependencies = ["integrity_coverage"]
+
+        self.params = {
+            "bcalmKmerSize": {
+                "default": 31,
+                "description":
+                    "size of a kmer"
+            },
+            "clearInput": {
+                "default": "false",
+                "description":
+                    "Permanently removes temporary input files. This option "
+                    "is only useful to remove temporary files in large "
+                    "workflows and prevents nextflow's resume functionality. "
+                    "Use with caution."
+	    }
+        }
+
+        self.directives = {"bcalm": {
+            "cpus": 4,
+            "memory": "{ 5.GB * task.attempt }",
+            "container": "quay.io/biocontainers/quast",
+            "version": "2.2.0",
+            "scratch": "true"
+        }}
+
 
 class Spades(Process):
     """Spades process template interface
diff --git a/flowcraft/generator/engine.py b/flowcraft/generator/engine.py
index f4083f3d..4115dc90 100644
--- a/flowcraft/generator/engine.py
+++ b/flowcraft/generator/engine.py
@@ -97,6 +97,7 @@
         "seq_typing": typing.SeqTyping,
         "sistr": typing.Sistr,
         "skesa": assembly.Skesa,
+        "bcalm": assembly.Bcalm,
         "spades": assembly.Spades,
         "split_assembly": meta.SplitAssembly,
         "trimmomatic": readsqc.Trimmomatic,
diff --git a/flowcraft/generator/templates/bcalm.nf b/flowcraft/generator/templates/bcalm.nf
new file mode 100644
index 00000000..7862f89c
--- /dev/null
+++ b/flowcraft/generator/templates/bcalm.nf
@@ -0,0 +1,30 @@
+# Check parameter
+if ( !params.bcalmKmerSize{{ param_id }}.toString().isNumber() ){
+    exit 1, "'bcalmKmerSize{{ param_id }}' parameter must be a number. Provided value: '${params.bcalmKmes%rSize{{ param_id }}}'"
+}
+
+# Clear
+clear = params.clearInput{{ param_id }} ? "true" : "false"
+checkpointClear_{{ pid }} = Channel.value(clear)
+
+process bcalm_{{ pid }} {
+    {% include "post.txt" ignore missing %}
+
+    tag { sample_id }
+    publishDir "results/assembly/bcalm_{{pid}}/$sample_id", pattern: "*.unitig.fa"
+    publishDir "reports/assembly/quast_{{pid}}/$sample_id"
+
+    input:
+    set sample_id, file(fastq) from {{input_channel}}
+    val KmerSize from Channel.value(params.bcalmKmerSize{{param_id}})
+    
+output:
+    file "*"
+    {% with task_name="bcalm" %}
+    {%- include "compiler_channels.txt" ignore missing -%}
+    {% endwith %}
+
+    script:
+    "bcalm -in $fastq -out unitig -kmer-size $KmerSize"
+}
+

From 86f7e60134cda4a24c1b35c5ad54877b8e3006a4 Mon Sep 17 00:00:00 2001
From: Marijon Pierre <pierre.marijon@inria.fr>
Date: Sun, 14 Oct 2018 22:02:15 +0200
Subject: [PATCH 2/7] bcalm: correct some mistake

---
 flowcraft/generator/engine.py          | 2 +-
 flowcraft/generator/templates/bcalm.nf | 8 +++-----
 2 files changed, 4 insertions(+), 6 deletions(-)

diff --git a/flowcraft/generator/engine.py b/flowcraft/generator/engine.py
index 4115dc90..c6071933 100644
--- a/flowcraft/generator/engine.py
+++ b/flowcraft/generator/engine.py
@@ -57,6 +57,7 @@
 process_map = {
         "abricate": annotation.Abricate,
         "assembly_mapping": ap.AssemblyMapping,
+        "bcalm": assembly.Bcalm,
         "bowtie": mapping.Bowtie,
         "card_rgi": annotation.CardRgi,
         "check_coverage": readsqc.CheckCoverage,
@@ -97,7 +98,6 @@
         "seq_typing": typing.SeqTyping,
         "sistr": typing.Sistr,
         "skesa": assembly.Skesa,
-        "bcalm": assembly.Bcalm,
         "spades": assembly.Spades,
         "split_assembly": meta.SplitAssembly,
         "trimmomatic": readsqc.Trimmomatic,
diff --git a/flowcraft/generator/templates/bcalm.nf b/flowcraft/generator/templates/bcalm.nf
index 7862f89c..c9a1bd7e 100644
--- a/flowcraft/generator/templates/bcalm.nf
+++ b/flowcraft/generator/templates/bcalm.nf
@@ -1,9 +1,9 @@
-# Check parameter
+// Check parameter
 if ( !params.bcalmKmerSize{{ param_id }}.toString().isNumber() ){
     exit 1, "'bcalmKmerSize{{ param_id }}' parameter must be a number. Provided value: '${params.bcalmKmes%rSize{{ param_id }}}'"
 }
 
-# Clear
+// Clear
 clear = params.clearInput{{ param_id }} ? "true" : "false"
 checkpointClear_{{ pid }} = Channel.value(clear)
 
@@ -11,15 +11,13 @@ process bcalm_{{ pid }} {
     {% include "post.txt" ignore missing %}
 
     tag { sample_id }
-    publishDir "results/assembly/bcalm_{{pid}}/$sample_id", pattern: "*.unitig.fa"
-    publishDir "reports/assembly/quast_{{pid}}/$sample_id"
 
     input:
     set sample_id, file(fastq) from {{input_channel}}
     val KmerSize from Channel.value(params.bcalmKmerSize{{param_id}})
     
 output:
-    file "*"
+    file "*.unitig.fa"
     {% with task_name="bcalm" %}
     {%- include "compiler_channels.txt" ignore missing -%}
     {% endwith %}

From f6724a5cea6f36c10c4f151f37f2c56f364ae191 Mon Sep 17 00:00:00 2001
From: Marijon Pierre <pierre.marijon@inria.fr>
Date: Sun, 14 Oct 2018 22:05:14 +0200
Subject: [PATCH 3/7] Add bcalm in changelog

---
 changelog.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/changelog.md b/changelog.md
index 5d136beb..db37ab97 100644
--- a/changelog.md
+++ b/changelog.md
@@ -17,6 +17,7 @@ which is particularly useful in very large workflows.
 
 ### New components
 - Added component `fast_ani`.
+- Added component `bcalm`.
 
 ### Minor/Other changes
 

From 2e4046622803503549553ecdb706e865a8131e46 Mon Sep 17 00:00:00 2001
From: Marijon Pierre <pierre.marijon@inria.fr>
Date: Sun, 14 Oct 2018 22:09:05 +0200
Subject: [PATCH 4/7] Typo correction

---
 flowcraft/generator/templates/bcalm.nf | 1 +
 1 file changed, 1 insertion(+)

diff --git a/flowcraft/generator/templates/bcalm.nf b/flowcraft/generator/templates/bcalm.nf
index c9a1bd7e..be7e5885 100644
--- a/flowcraft/generator/templates/bcalm.nf
+++ b/flowcraft/generator/templates/bcalm.nf
@@ -11,6 +11,7 @@ process bcalm_{{ pid }} {
     {% include "post.txt" ignore missing %}
 
     tag { sample_id }
+    publishDir "reports/assembly/quast_{{pid}}/$sample_id"
 
     input:
     set sample_id, file(fastq) from {{input_channel}}

From 90a99e9e1bcace6c177160c9cfd8586a84f4ab61 Mon Sep 17 00:00:00 2001
From: Marijon Pierre <pierre.marijon@inria.fr>
Date: Fri, 26 Oct 2018 15:41:19 +0200
Subject: [PATCH 5/7] Solve @ODiogoSilva comments

---
 flowcraft/generator/templates/bcalm.nf | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/flowcraft/generator/templates/bcalm.nf b/flowcraft/generator/templates/bcalm.nf
index be7e5885..700487a0 100644
--- a/flowcraft/generator/templates/bcalm.nf
+++ b/flowcraft/generator/templates/bcalm.nf
@@ -24,6 +24,15 @@ output:
     {% endwith %}
 
     script:
-    "bcalm -in $fastq -out unitig -kmer-size $KmerSize"
+    """
+    {
+	bcalm -in $fastq -out unitig -kmer-size $KmerSize"
+
+  	if [ "$clear" = "true" ];
+	then
+    	    find . -type f  -print | egrep "work/.*(h5)|(glue)" | xargs -L 1 rm
+	fi
+    }
+    """
 }
 

From 21aa26e5f50707542dc97c55adb52e89f316377e Mon Sep 17 00:00:00 2001
From: Marijon Pierre <pierre.marijon@inria.fr>
Date: Fri, 26 Oct 2018 15:42:31 +0200
Subject: [PATCH 6/7] Solve @tiagofilipe12 comments

---
 changelog.md | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/changelog.md b/changelog.md
index db37ab97..582ae4ec 100644
--- a/changelog.md
+++ b/changelog.md
@@ -2,6 +2,8 @@
 
 ## Changes in upcoming release (`dev` branch) 
 
+- Added component `bcalm`.
+
 ## 1.3.1
 
 ### Features
@@ -17,7 +19,6 @@ which is particularly useful in very large workflows.
 
 ### New components
 - Added component `fast_ani`.
-- Added component `bcalm`.
 
 ### Minor/Other changes
 

From 9bf6786aedf1734401da40d4c9fd651f39f60adb Mon Sep 17 00:00:00 2001
From: Marijon Pierre <pierre.marijon@inria.fr>
Date: Fri, 26 Oct 2018 15:42:53 +0200
Subject: [PATCH 7/7] Add good docker image with good version number

---
 flowcraft/generator/components/assembly.py | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/flowcraft/generator/components/assembly.py b/flowcraft/generator/components/assembly.py
index 1073a83e..e2a12474 100644
--- a/flowcraft/generator/components/assembly.py
+++ b/flowcraft/generator/components/assembly.py
@@ -22,8 +22,6 @@ def __init__(self, **kwargs):
         self.input_type = "fastq"
         self.output_type = "fasta"
 
-        self.dependencies = ["integrity_coverage"]
-
         self.params = {
             "bcalmKmerSize": {
                 "default": 31,
@@ -43,8 +41,8 @@ def __init__(self, **kwargs):
         self.directives = {"bcalm": {
             "cpus": 4,
             "memory": "{ 5.GB * task.attempt }",
-            "container": "quay.io/biocontainers/quast",
-            "version": "2.2.0",
+            "container": "quay.io/biocontainers/bcalm",
+            "version": "2.2.0--hd28b015_2",
             "scratch": "true"
         }}