🔀 Merge pull request #54 from cnr-ibba/dev

🔖 pipeline release v0.5.2
cnr-ibba · Dec 21, 2023 · f3fa36e · f3fa36e
2 parents db2db3e + 5179306
commit f3fa36e
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diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
@@ -14,9 +14,9 @@ jobs:
   EditorConfig:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
 
       - name: Install editorconfig-checker
         run: npm install -g editorconfig-checker
@@ -27,9 +27,9 @@ jobs:
   Prettier:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
 
       - name: Install Prettier
         run: npm install -g prettier
@@ -40,7 +40,7 @@ jobs:
   PythonBlack:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Check code lints with Black
         uses: psf/black@stable
@@ -71,7 +71,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1

diff --git a/conf/modules.config b/conf/modules.config
@@ -118,6 +118,7 @@ process {
     }
 
     withName: PICARD_MARKDUPLICATES {
+        ext.args = "--CREATE_INDEX"
         publishDir = [
             path: { "${params.outdir}/bam_files" },
             mode: params.publish_dir_mode,

diff --git a/lib/NfcoreTemplate.groovy b/lib/NfcoreTemplate.groovy
@@ -4,6 +4,7 @@
 
 import org.yaml.snakeyaml.Yaml
 import groovy.json.JsonOutput
+import nextflow.extension.FilesEx
 
 class NfcoreTemplate {
 
@@ -141,12 +142,14 @@ class NfcoreTemplate {
             try {
                 if (params.plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') }
                 // Try to send HTML e-mail using sendmail
+                def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html")
+                sendmail_tf.withWriter { w -> w << sendmail_html }
                 [ 'sendmail', '-t' ].execute() << sendmail_html
                 log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (sendmail)-"
             } catch (all) {
                 // Catch failures and try with plaintext
                 def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ]
-                if ( mqc_report.size() <= max_multiqc_email_size.toBytes() ) {
+                if ( mqc_report != null && mqc_report.size() <= max_multiqc_email_size.toBytes() ) {
                     mail_cmd += [ '-A', mqc_report ]
                 }
                 mail_cmd.execute() << email_html
@@ -155,14 +158,16 @@ class NfcoreTemplate {
         }
 
         // Write summary e-mail HTML to a file
-        def output_d = new File("${params.outdir}/pipeline_info/")
-        if (!output_d.exists()) {
-            output_d.mkdirs()
-        }
-        def output_hf = new File(output_d, "pipeline_report.html")
+        def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html")
         output_hf.withWriter { w -> w << email_html }
-        def output_tf = new File(output_d, "pipeline_report.txt")
+        FilesEx.copyTo(output_hf.toPath(), "${params.outdir}/pipeline_info/pipeline_report.html");
+        output_hf.delete()
+
+        // Write summary e-mail TXT to a file
+        def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt")
         output_tf.withWriter { w -> w << email_txt }
+        FilesEx.copyTo(output_tf.toPath(), "${params.outdir}/pipeline_info/pipeline_report.txt");
+        output_tf.delete()
     }
 
     //
@@ -227,15 +232,14 @@ class NfcoreTemplate {
     // Dump pipeline parameters in a json file
     //
     public static void dump_parameters(workflow, params) {
-        def output_d = new File("${params.outdir}/pipeline_info/")
-        if (!output_d.exists()) {
-            output_d.mkdirs()
-        }
-
         def timestamp  = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
-        def output_pf  = new File(output_d, "params_${timestamp}.json")
+        def filename   = "params_${timestamp}.json"
+        def temp_pf    = new File(workflow.launchDir.toString(), ".${filename}")
         def jsonStr    = JsonOutput.toJson(params)
-        output_pf.text = JsonOutput.prettyPrint(jsonStr)
+        temp_pf.text   = JsonOutput.prettyPrint(jsonStr)
+
+        FilesEx.copyTo(temp_pf.toPath(), "${params.outdir}/pipeline_info/params_${timestamp}.json")
+        temp_pf.delete()
     }
 
     //

diff --git a/modules.json b/modules.json
@@ -7,27 +7,22 @@
         "cnr-ibba": {
           "bamaddrg": {
             "branch": "master",
-            "git_sha": "603030624cc426e58d6f2d6a44ff8c7d5cb047b1",
+            "git_sha": "0df6dad6fccf03d5bf452766dd1ea9795654338b",
             "installed_by": ["modules"]
           },
           "freebayes/chunk": {
             "branch": "master",
-            "git_sha": "e28cb1426b148bd8e5459910cf3354fe2b5f8d19",
+            "git_sha": "03189b5139b1112cc869e8b78b3b6f82c595d4df",
             "installed_by": ["modules"]
           },
           "freebayes/splitbam": {
             "branch": "master",
-            "git_sha": "fa93794d74e9508fb856b35c5826a7e93fbae990",
-            "installed_by": ["modules"]
-          },
-          "samtools/coverage": {
-            "branch": "master",
-            "git_sha": "603030624cc426e58d6f2d6a44ff8c7d5cb047b1",
+            "git_sha": "03189b5139b1112cc869e8b78b3b6f82c595d4df",
             "installed_by": ["modules"]
           },
           "seqkit/rmdup": {
             "branch": "master",
-            "git_sha": "f4c847049adcd3135e6e67fb469af12e05952791",
+            "git_sha": "c101f87859323fe184912c12a17404149a2a9ddd",
             "installed_by": ["modules"]
           }
         }
@@ -38,77 +33,97 @@
         "nf-core": {
           "bcftools/concat": {
             "branch": "master",
-            "git_sha": "78cf39939fbe160a1410c44a6c5946f9a4c56e7e",
+            "git_sha": "44096c08ffdbc694f5f92ae174ea0f7ba0f37e09",
             "installed_by": ["modules"]
           },
           "bcftools/norm": {
             "branch": "master",
-            "git_sha": "78cf39939fbe160a1410c44a6c5946f9a4c56e7e",
+            "git_sha": "44096c08ffdbc694f5f92ae174ea0f7ba0f37e09",
+            "installed_by": ["modules"]
+          },
+          "bcftools/stats": {
+            "branch": "master",
+            "git_sha": "44096c08ffdbc694f5f92ae174ea0f7ba0f37e09",
             "installed_by": ["modules"]
           },
           "bwa/index": {
             "branch": "master",
-            "git_sha": "9518fa4f65f3fb8cde24fde7d40333b39ec8fd65",
+            "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
             "installed_by": ["modules"]
           },
           "bwa/mem": {
             "branch": "master",
-            "git_sha": "cf5b9c30a2adacc581793afb79fae5f5b50bed01",
+            "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
             "installed_by": ["modules"]
           },
           "cat/fastq": {
             "branch": "master",
-            "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+            "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
             "installed_by": ["modules"]
           },
           "custom/dumpsoftwareversions": {
             "branch": "master",
-            "git_sha": "8022c68e7403eecbd8ba9c49496f69f8c49d50f0",
+            "git_sha": "bba7e362e4afead70653f84d8700588ea28d0f9e",
             "installed_by": ["modules"]
           },
           "fastqc": {
             "branch": "master",
-            "git_sha": "3dd73937b084b547f9272bc901e0f120a7913fd8",
+            "git_sha": "65ad3e0b9a4099592e1102e92e10455dc661cf53",
             "installed_by": ["modules"]
           },
           "multiqc": {
             "branch": "master",
-            "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+            "git_sha": "4ab13872435962dadc239979554d13709e20bf29",
             "installed_by": ["modules"]
           },
           "picard/markduplicates": {
             "branch": "master",
-            "git_sha": "eca65aa4a5e2e192ac44d6962c8f9260f314ffb8",
+            "git_sha": "20b0918591d4ba20047d7e13e5094bcceba81447",
+            "installed_by": ["modules"]
+          },
+          "samtools/coverage": {
+            "branch": "master",
+            "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
             "installed_by": ["modules"]
           },
           "samtools/faidx": {
             "branch": "master",
-            "git_sha": "cf5b9c30a2adacc581793afb79fae5f5b50bed01",
+            "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
             "installed_by": ["modules"]
           },
           "samtools/flagstat": {
             "branch": "master",
-            "git_sha": "cf5b9c30a2adacc581793afb79fae5f5b50bed01",
+            "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
+            "installed_by": ["modules"]
+          },
+          "samtools/idxstats": {
+            "branch": "master",
+            "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
             "installed_by": ["modules"]
           },
           "samtools/index": {
             "branch": "master",
-            "git_sha": "cf5b9c30a2adacc581793afb79fae5f5b50bed01",
+            "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
+            "installed_by": ["modules"]
+          },
+          "samtools/stats": {
+            "branch": "master",
+            "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
             "installed_by": ["modules"]
           },
           "tabix/bgzip": {
             "branch": "master",
-            "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+            "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
             "installed_by": ["modules"]
           },
           "tabix/tabix": {
             "branch": "master",
-            "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+            "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
             "installed_by": ["modules"]
           },
           "trimgalore": {
             "branch": "master",
-            "git_sha": "b51a69e30973c71950225c817ad07a3337d22c40",
+            "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
             "installed_by": ["modules"]
           }
         }

diff --git a/modules/cnr-ibba/bamaddrg/environment.yml b/modules/cnr-ibba/bamaddrg/environment.yml
@@ -0,0 +1,7 @@
+name: bamaddrg
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::bamaddrg=9baba65f88228e55639689a3cea38dd150e6284f
diff --git a/modules/cnr-ibba/bamaddrg/main.nf b/modules/cnr-ibba/bamaddrg/main.nf
@@ -3,10 +3,10 @@ process BAMADDRG {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::bamaddrg=9baba65f88228e55639689a3cea38dd150e6284f" : null)
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bamaddrg:9baba65f88228e55639689a3cea38dd150e6284f--ha89c123_1':
-        'quay.io/biocontainers/bamaddrg:9baba65f88228e55639689a3cea38dd150e6284f--ha89c123_1' }"
+        'biocontainers/bamaddrg:9baba65f88228e55639689a3cea38dd150e6284f--ha89c123_1' }"
 
     input:
     tuple val(meta), path(bam)

diff --git a/modules/cnr-ibba/bamaddrg/meta.yml b/modules/cnr-ibba/bamaddrg/meta.yml
@@ -2,14 +2,17 @@ name: "bamaddrg"
 description: adds read groups to input BAM files
 keywords:
   - sort
+  - add
+  - read
+  - group
+  - bam
 tools:
   - "bamaddrg":
       description: "Add read group to BAM files"
       homepage: "https://github.com/ekg/bamaddrg"
       documentation: "https://github.com/ekg/bamaddrg"
       tool_dev_url: "https://github.com/ekg/bamaddrg"
-      doi: ""
-      licence: "['MIT']"
+      licence: ["MIT"]
 
 input:
   # Only when we have meta

diff --git a/modules/cnr-ibba/freebayes/chunk/environment.yml b/modules/cnr-ibba/freebayes/chunk/environment.yml
@@ -0,0 +1,7 @@
+name: freebayes_chunk
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::freebayes=1.3.6
diff --git a/modules/cnr-ibba/freebayes/chunk/main.nf b/modules/cnr-ibba/freebayes/chunk/main.nf
@@ -4,18 +4,18 @@ process FREEBAYES_CHUNK {
     label 'process_low'
     label 'error_retry'
 
-    conda (params.enable_conda ? "bioconda::freebayes=1.3.6" : null)
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/freebayes:1.3.6--hb089aa1_0':
-        'quay.io/biocontainers/freebayes:1.3.6--hb089aa1_0' }"
+        'biocontainers/freebayes:1.3.6--hb089aa1_0' }"
 
     input:
-    tuple val(meta), val(region)
-    tuple val(sample_meta), path(bam)
-    tuple val(sample_meta), path(bai)
-    tuple val(sample_meta), path(bam_list)
-    path(genome_fasta)
-    path(genome_fasta_fai)
+    tuple val(meta),  val(region)
+    tuple val(meta2), path(bam)
+    tuple val(meta2), path(bai)
+    tuple val(meta2), path(bam_list)
+    tuple val(meta3), path(genome_fasta)
+    tuple val(meta3), path(genome_fasta_fai)
 
     output:
     tuple val(meta), path("*.vcf.gz")     , emit: vcf