From 631c115e1003fc7cb9b0c893bf7cde761f4287ef Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Mon, 21 Mar 2022 14:58:19 +0000
Subject: [PATCH] Adds PoC of untarring system

---
 conf/modules.config                    |  2 +-
 modules.json                           |  2 +-
 modules/nf-core/modules/untar/main.nf  | 10 +++++-----
 modules/nf-core/modules/untar/meta.yml | 10 ++++++++++
 subworkflows/local/db_check.nf         |  9 +++++----
 5 files changed, 22 insertions(+), 11 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 9e334bc..620ae1d 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -82,7 +82,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/kraken2/${meta.db_name}" },
             mode: 'copy',
-            pattern: '.{fastq.gz,txt}'
+            pattern: '*.{fastq.gz,txt}'
         ]
         ext.args = { "${meta.db_params}" }
         ext.when = params.run_kraken2
diff --git a/modules.json b/modules.json
index 9a7f1df..96a43d8 100644
--- a/modules.json
+++ b/modules.json
@@ -25,7 +25,7 @@
                 "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
             },
             "untar": {
-                "git_sha": "7ec09d0ef4df89617baacc9b2dafcddb7cd4b05a"
+                "git_sha": "e080f4c8acf5760039ed12ec1f206170f3f9a918"
             }
         }
     }
diff --git a/modules/nf-core/modules/untar/main.nf b/modules/nf-core/modules/untar/main.nf
index bbae948..dc43fb7 100644
--- a/modules/nf-core/modules/untar/main.nf
+++ b/modules/nf-core/modules/untar/main.nf
@@ -8,19 +8,19 @@ process UNTAR {
         'biocontainers/biocontainers:v1.2.0_cv1' }"
 
     input:
-    path archive
+    tuple val(meta), path(archive)
 
     output:
-    path "$untar"      , emit: untar
-    path "versions.yml", emit: versions
+    tuple val(meta), path("$untar"), emit: untar
+    path "versions.yml"            , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
+    def args  = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
-    untar        = archive.toString() - '.tar.gz'
+    untar     = archive.toString() - '.tar.gz'
     """
     tar \\
         -xzvf \\
diff --git a/modules/nf-core/modules/untar/meta.yml b/modules/nf-core/modules/untar/meta.yml
index e877a97..d426919 100644
--- a/modules/nf-core/modules/untar/meta.yml
+++ b/modules/nf-core/modules/untar/meta.yml
@@ -10,11 +10,21 @@ tools:
       documentation: https://www.gnu.org/software/tar/manual/
       licence: ["GPL-3.0-or-later"]
 input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
   - archive:
       type: file
       description: File to be untar
       pattern: "*.{tar}.{gz}"
 output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
   - untar:
       type: file
       description:
diff --git a/subworkflows/local/db_check.nf b/subworkflows/local/db_check.nf
index 6f061d7..641108d 100644
--- a/subworkflows/local/db_check.nf
+++ b/subworkflows/local/db_check.nf
@@ -3,6 +3,7 @@
 //
 
 include { DATABASE_CHECK } from '../../modules/local/database_check'
+include { UNTAR          } from '../../modules/nf-core/modules/untar/main'
 
 workflow DB_CHECK {
     take:
@@ -17,19 +18,19 @@ workflow DB_CHECK {
         .dump(tag: "db_split_csv_out")
         .map { create_db_channels(it) }
         .dump(tag: "db_channel_prepped")
-        .set{ dbs }
-
 
     parsed_samplesheet
         .branch {
-            untar: it[0]['db_path'].toString().endsWith(".tar.gz")
+            untar: it[1].toString().endsWith(".tar.gz")
             skip: true
         }
         .set{ ch_dbs_for_untar }
 
+    // TODO Filter to only run UNTAR on DBs of tools actually using?
+    // TODO make optional whether to save
     UNTAR ( ch_dbs_for_untar.untar )
 
-    ch_final_dbs = ch_dbs_for_untar.skip.mix( ch_dbs_untarred )
+    ch_final_dbs = ch_dbs_for_untar.skip.mix( UNTAR.out.untar )
 
     emit:
     dbs = ch_final_dbs                        // channel: [ val(meta), [ db ] ]