Update busco to v5.4.3 and tar small files (#1970)

* Update busco to v5.4.3 and tar small files

* Fix file contain strings

* Swap md5sums to contains for variable files

modules/busco/main.nf

@@ -2,10 +2,10 @@ process BUSCO {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::busco=5.3.2" : null)
+    conda (params.enable_conda ? "bioconda::busco=5.4.3" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/busco:5.3.2--pyhdfd78af_0':
-        'quay.io/biocontainers/busco:5.3.2--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/busco:5.4.3--pyhdfd78af_0':
+        'quay.io/biocontainers/busco:5.4.3--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path('tmp_input/*')

tests/modules/busco/main.nf

@@ -15,7 +15,7 @@ workflow test_busco_genome_single_fasta {
         input,
         ['bacteria_odb10', 'bacteroidetes_odb10'],  // Launch with 'auto' to use --auto-lineage, and specified lineages // 'auto' removed from test due to memory issues
         [], // Download busco lineage
-        [], // No config
+        [] // No config
     )
 
     /* Output tree:
@@ -63,84 +63,6 @@ workflow test_busco_genome_single_fasta {
     │       └── busco.log
     ├── test-bacteroidetes_odb10-busco.batch_summary.txt -> /tmp/tmpza_0dth3/6a/e95a0cd21785ce33d63b8f73a68a51/test-bacteroidetes_odb10-busco.batch_summary.txt
     └── versions.yml -> /tmp/tmpza_0dth3/6a/e95a0cd21785ce33d63b8f73a68a51/versions.yml
-
-    Former Output tree -w 'auto':
-    /tmp/tmp846crjv2/busco/
-    ├── short_summary.generic.bacteria_odb10.genome.fna.json -> /tmp/tmpi6af66j1/18/8be22ecd7a71471ff5082bd512972b/short_summary.generic.bacteria_odb10.genome.fna.json
-    ├── short_summary.generic.bacteria_odb10.genome.fna.txt -> /tmp/tmpi6af66j1/18/8be22ecd7a71471ff5082bd512972b/short_summary.generic.bacteria_odb10.genome.fna.txt
-    ├── short_summary.specific.bacteria_odb10.genome.fna.json -> /tmp/tmpi6af66j1/45/107812e983a8e695c380ebc215e7d9/short_summary.specific.bacteria_odb10.genome.fna.json
-    ├── short_summary.specific.bacteria_odb10.genome.fna.txt -> /tmp/tmpi6af66j1/45/107812e983a8e695c380ebc215e7d9/short_summary.specific.bacteria_odb10.genome.fna.txt
-    ├── short_summary.specific.bacteroidales_odb10.genome.fna.json -> /tmp/tmpi6af66j1/18/8be22ecd7a71471ff5082bd512972b/short_summary.specific.bacteroidales_odb10.genome.fna.json
-    ├── short_summary.specific.bacteroidales_odb10.genome.fna.txt -> /tmp/tmpi6af66j1/18/8be22ecd7a71471ff5082bd512972b/short_summary.specific.bacteroidales_odb10.genome.fna.txt
-    ├── short_summary.specific.bacteroidetes_odb10.genome.fna.json -> /tmp/tmpi6af66j1/a2/eb4a34894f3ac5554759ad6c9f652b/short_summary.specific.bacteroidetes_odb10.genome.fna.json
-    ├── short_summary.specific.bacteroidetes_odb10.genome.fna.txt -> /tmp/tmpi6af66j1/a2/eb4a34894f3ac5554759ad6c9f652b/short_summary.specific.bacteroidetes_odb10.genome.fna.txt
-    ├── test-auto-busco -> /tmp/tmpi6af66j1/18/8be22ecd7a71471ff5082bd512972b/test-auto-busco/
-    │   ├── genome.fna/
-    │   │   ├── auto_lineage/
-    │   │   │   ├── run_archaea_odb10/
-    │   │   │   ├── run_bacteria_odb10/
-    │   │   │   └── run_eukaryota_odb10/
-    │   │   ├── logs/
-    │   │   │   ├── hmmsearch_err.log
-    │   │   │   ├── hmmsearch_out.log
-    │   │   │   ├── metaeuk_err.log
-    │   │   │   ├── metaeuk_out.log
-    │   │   │   ├── prodigal_err.log
-    │   │   │   ├── prodigal_out.log
-    │   │   │   ├── sepp_err.log
-    │   │   │   └── sepp_out.log
-    │   │   ├── prodigal_output/
-    │   │   │   └── predicted_genes/
-    │   │   ├── run_bacteria_odb10 -> /tmp/tmpi6af66j1/18/8be22ecd7a71471ff5082bd512972b/test-auto-busco/genome.fna/auto_lineage/run_bacteria_odb10/  [recursive, not followed]
-    │   │   └── run_bacteroidales_odb10/
-    │   │       ├── busco_sequences/
-    │   │       ├── full_table.tsv
-    │   │       ├── hmmer_output/
-    │   │       ├── missing_busco_list.tsv
-    │   │       ├── short_summary.json
-    │   │       └── short_summary.txt
-    │   └── logs/
-    │       └── busco.log
-    ├── test-auto-busco.batch_summary.txt -> /tmp/tmpi6af66j1/18/8be22ecd7a71471ff5082bd512972b/test-auto-busco.batch_summary.txt
-    ├── test-bacteria_odb10-busco -> /tmp/tmpi6af66j1/45/107812e983a8e695c380ebc215e7d9/test-bacteria_odb10-busco/
-    │   ├── genome.fna/
-    │   │   ├── logs/
-    │   │   │   ├── hmmsearch_err.log
-    │   │   │   ├── hmmsearch_out.log
-    │   │   │   ├── prodigal_err.log
-    │   │   │   └── prodigal_out.log
-    │   │   ├── prodigal_output/
-    │   │   │   └── predicted_genes/
-    │   │   └── run_bacteria_odb10/
-    │   │       ├── busco_sequences/
-    │   │       ├── full_table.tsv
-    │   │       ├── hmmer_output/
-    │   │       ├── missing_busco_list.tsv
-    │   │       ├── short_summary.json
-    │   │       └── short_summary.txt
-    │   └── logs/
-    │       └── busco.log
-    ├── test-bacteria_odb10-busco.batch_summary.txt -> /tmp/tmpi6af66j1/45/107812e983a8e695c380ebc215e7d9/test-bacteria_odb10-busco.batch_summary.txt
-    ├── test-bacteroidetes_odb10-busco -> /tmp/tmpi6af66j1/a2/eb4a34894f3ac5554759ad6c9f652b/test-bacteroidetes_odb10-busco/
-    │   ├── genome.fna/
-    │   │   ├── logs/
-    │   │   │   ├── hmmsearch_err.log
-    │   │   │   ├── hmmsearch_out.log
-    │   │   │   ├── prodigal_err.log
-    │   │   │   └── prodigal_out.log
-    │   │   ├── prodigal_output/
-    │   │   │   └── predicted_genes/
-    │   │   └── run_bacteroidetes_odb10/
-    │   │       ├── busco_sequences/
-    │   │       ├── full_table.tsv
-    │   │       ├── hmmer_output/
-    │   │       ├── missing_busco_list.tsv
-    │   │       ├── short_summary.json
-    │   │       └── short_summary.txt
-    │   └── logs/
-    │       └── busco.log
-    ├── test-bacteroidetes_odb10-busco.batch_summary.txt -> /tmp/tmpi6af66j1/a2/eb4a34894f3ac5554759ad6c9f652b/test-bacteroidetes_odb10-busco.batch_summary.txt
-    └── versions.yml -> /tmp/tmpi6af66j1/18/8be22ecd7a71471ff5082bd512972b/versions.yml
     */
 
 }
@@ -159,7 +81,7 @@ workflow test_busco_genome_multi_fasta {
         input,
         'bacteria_odb10',
         [], // Download busco lineage
-        [], // No config
+        [] // No config
     )
 
     /* Output tree:
@@ -218,7 +140,7 @@ workflow test_busco_eukaryote_metaeuk {
         input,
         'eukaryota_odb10',
         [], // Download busco lineage
-        [], // No config
+        [] // No config
     )
 
     /* Output tree:
@@ -259,7 +181,7 @@ workflow test_busco_eukaryote_augustus {
         input,
         'eukaryota_odb10',
         [], // Download busco lineage
-        [], // No config
+        [] // No config
     )
 
     /* Output tree:
@@ -303,7 +225,7 @@ workflow test_busco_protein {
         input,
         'bacteria_odb10',
         [], // Download busco lineage
-        [], // No config
+        [] // No config
     )
 
     /* Output tree:
@@ -339,7 +261,7 @@ workflow test_busco_transcriptome {
         input,
         'bacteria_odb10',
         [], // Download busco lineage
-        [], // No config
+        [] // No config
     )
 
     /* Output tree:

tests/modules/busco/nextflow.config

@@ -3,26 +3,26 @@ process {
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
 
     withName: 'test_busco_genome_single_fasta:BUSCO' {
-        ext.args = '--mode genome'
+        ext.args = '--mode genome --tar'
     }
 
     withName: 'test_busco_genome_multi_fasta:BUSCO' {
-        ext.args = '--mode genome'
+        ext.args = '--mode genome --tar'
     }
 
     withName: 'test_busco_eukaryote_metaeuk:BUSCO' {
-        ext.args = '--mode genome'
+        ext.args = '--mode genome --tar'
     }
 
     withName: 'test_busco_eukaryote_augustus:BUSCO' {
-        ext.args = '--mode genome --augustus'
+        ext.args = '--mode genome --augustus --tar'
     }
 
     withName: 'test_busco_protein:BUSCO' {
-        ext.args = '--mode proteins'
+        ext.args = '--mode proteins --tar'
     }
 
     withName: 'test_busco_transcriptome:BUSCO'{
-        ext.args = '--mode transcriptome'
+        ext.args = '--mode transcriptome --tar'
     }
 }

tests/modules/busco/test.yml

@@ -1,12 +1,11 @@
 - name: busco test_busco_genome_single_fasta
-  command: nextflow run tests/modules/busco -entry test_busco_genome_single_fasta -c tests/config/nextflow.config
+  command: nextflow run ./tests/modules/busco -entry test_busco_genome_single_fasta -c ./tests/config/nextflow.config  -c ./tests/modules/busco/nextflow.config
   tags:
     - busco
   files:
     - path: output/busco/short_summary.specific.bacteria_odb10.genome.fna.json
       contains:
         - "one_line_summary"
-        - "input_file"
         - "mode"
         - "dataset"
     - path: output/busco/short_summary.specific.bacteria_odb10.genome.fna.txt
@@ -20,7 +19,6 @@
     - path: output/busco/short_summary.specific.bacteroidetes_odb10.genome.fna.json
       contains:
         - "one_line_summary"
-        - "input_file"
         - "mode"
         - "dataset"
     - path: output/busco/short_summary.specific.bacteroidetes_odb10.genome.fna.txt
@@ -32,21 +30,142 @@
         - "Missing BUSCOs"
         - "Dependencies and versions"
     - path: output/busco/test-bacteria_odb10-busco.batch_summary.txt
-      md5sum: e50690742e9ae6abdd2bf99334ff9e12
+      md5sum: bc2440f8a68d7fbf931ff911c1c3fdfa
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/logs/bbtools_err.log
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/logs/bbtools_out.log
+      contains:
+        - "IUPAC"
+        - "genome scaffold"
+        - "Coverage"
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/logs/hmmsearch_err.log
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/logs/hmmsearch_out.log
+      contains:
+        - "# hmmsearch :: search profile(s) against a sequence database"
+        - "# target sequence database:"
+        - "Internal pipeline statistics summary:"
+        - "[ok]"
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/logs/prodigal_err.log
+      md5sum: 538510cfc7483498210f01e53fe035ad
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/logs/prodigal_out.log
+      md5sum: 61050b0706addc9498b2088a2d6efa9a
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/.checkpoint
+      contains:
+        - "Tool: prodigal"
+        - "Completed"
+        - "jobs"
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/predicted_genes/predicted.faa
+      md5sum: 836e9a80d33d8b89168f07ddc13ee991
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/predicted_genes/predicted.fna
+      md5sum: 20eeb75f86842e6e136f02bca8b73a9f
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11.faa
+      md5sum: 836e9a80d33d8b89168f07ddc13ee991
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11.fna
+      md5sum: 20eeb75f86842e6e136f02bca8b73a9f
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11_err.log
+      md5sum: 538510cfc7483498210f01e53fe035ad
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11_out.log
+      md5sum: 61050b0706addc9498b2088a2d6efa9a
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/.bbtools_output/.checkpoint
+      contains:
+        - "Tool: bbtools"
+        - "Completed"
+        - "jobs"
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/busco_sequences/fragmented_busco_sequences.tar.gz
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/busco_sequences/multi_copy_busco_sequences.tar.gz
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/busco_sequences/single_copy_busco_sequences.tar.gz
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/full_table.tsv
+      md5sum: 275a7ece09ef61aa59ee7a811289e3d8
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/hmmer_output.tar.gz
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/missing_busco_list.tsv
+      md5sum: ab574cde031a3fbff471976ea61e215d
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/short_summary.json
+      contains:
+        - "one_line_summary"
+        - "mode"
+        - "lineage_dataset"
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/short_summary.txt
+      contains:
+        - "# BUSCO version is:"
+        - "Results:"
+        - "busco:"
+    - path: output/busco/test-bacteria_odb10-busco/logs/busco.log
+      contains:
+        - "DEBUG:busco.run_BUSCO"
+        - "Results from dataset"
+        - "how to cite BUSCO"
     - path: output/busco/test-bacteroidetes_odb10-busco.batch_summary.txt
-      md5sum: 4c1b2c4317c88398eddc30877ed740d9
-    - path: output/busco/versions.yml
-      md5sum: 8aa830f71587d859df35c6cfab59f35d
+      md5sum: 5ad8ecfbf4058b059e5edeb9170fc683
+    - path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/logs/bbtools_err.log
+    - path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/logs/bbtools_out.log
+      contains:
+        - "IUPAC"
+        - "genome scaffold"
+        - "Coverage"
+    - path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/logs/hmmsearch_err.log
+    - path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/logs/hmmsearch_out.log
+      contains:
+        - "# hmmsearch :: search profile(s) against a sequence database"
+        - "# target sequence database:"
+        - "Internal pipeline statistics summary:"
+        - "[ok]"
+    - path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/logs/prodigal_err.log
+      md5sum: 538510cfc7483498210f01e53fe035ad
+    - path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/logs/prodigal_out.log
+      md5sum: 61050b0706addc9498b2088a2d6efa9a
+    - path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/prodigal_output/.checkpoint
+      contains:
+        - "Tool: prodigal"
+        - "Completed"
+        - "jobs"
+    - path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/prodigal_output/predicted_genes/predicted.faa
+      md5sum: 836e9a80d33d8b89168f07ddc13ee991
+    - path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/prodigal_output/predicted_genes/predicted.fna
+      md5sum: 20eeb75f86842e6e136f02bca8b73a9f
+    - path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11.faa
+      md5sum: 836e9a80d33d8b89168f07ddc13ee991
+    - path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11.fna
+      md5sum: 20eeb75f86842e6e136f02bca8b73a9f
+    - path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11_err.log
+      md5sum: 538510cfc7483498210f01e53fe035ad
+    - path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11_out.log
+      md5sum: 61050b0706addc9498b2088a2d6efa9a
+    - path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/run_bacteroidetes_odb10/.bbtools_output/.checkpoint
+      contains:
+        - "Tool: bbtools"
+        - "Completed"
+        - "jobs"
+    - path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/run_bacteroidetes_odb10/busco_sequences/fragmented_busco_sequences.tar.gz
+    - path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/run_bacteroidetes_odb10/busco_sequences/multi_copy_busco_sequences.tar.gz
+    - path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/run_bacteroidetes_odb10/busco_sequences/single_copy_busco_sequences.tar.gz
+    - path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/run_bacteroidetes_odb10/full_table.tsv
+      md5sum: 2360bb06f7171dafaa7ebf879789689b
+    - path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/run_bacteroidetes_odb10/hmmer_output.tar.gz
+    - path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/run_bacteroidetes_odb10/missing_busco_list.tsv
+      md5sum: e1fb12cf416448d35fbc5c508065963a
+    - path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/run_bacteroidetes_odb10/short_summary.json
+      contains:
+        - "one_line_summary"
+        - "mode"
+        - "lineage_dataset"
+    - path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/run_bacteroidetes_odb10/short_summary.txt
+      contains:
+        - "# BUSCO version is:"
+        - "Results:"
+        - "busco:"
+    - path: output/busco/test-bacteroidetes_odb10-busco/logs/busco.log
+      contains:
+        - "DEBUG:busco.run_BUSCO"
+        - "Results from dataset"
+        - "how to cite BUSCO"
 
 - name: busco test_busco_genome_multi_fasta
-  command: nextflow run tests/modules/busco -entry test_busco_genome_multi_fasta -c tests/config/nextflow.config
+  command: nextflow run ./tests/modules/busco -entry test_busco_genome_multi_fasta -c ./tests/config/nextflow.config  -c ./tests/modules/busco/nextflow.config
   tags:
     - busco
   files:
     - path: output/busco/short_summary.specific.bacteria_odb10.genome.fasta.json
       contains:
         - "one_line_summary"
-        - "input_file"
         - "mode"
         - "dataset"
     - path: output/busco/short_summary.specific.bacteria_odb10.genome.fasta.txt
@@ -60,7 +179,6 @@
     - path: output/busco/short_summary.specific.bacteria_odb10.genome.fna.json
       contains:
         - "one_line_summary"
-        - "input_file"
         - "mode"
         - "dataset"
     - path: output/busco/short_summary.specific.bacteria_odb10.genome.fna.txt
@@ -74,28 +192,145 @@
     - path: output/busco/test-bacteria_odb10-busco.batch_summary.txt
       contains:
         - "Input_file"
-        - "Dataset"
-        - "Complete"
-        - "Single"
-        - "Duplicated"
-        - "Fragmented"
-        - "Missing"
-        - "n_markers"
-        - "genome.fasta"
         - "genome.fna"
+        - "genome.fasta"
         - "bacteria_odb10"
-    - path: output/busco/versions.yml
-      md5sum: 9a959eb0a1f765777dff1ea2f5c139c0
+    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/logs/bbtools_err.log
+    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/logs/bbtools_out.log
+      contains:
+        - "IUPAC"
+        - "genome scaffold"
+        - "Coverage"
+    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/logs/hmmsearch_err.log
+    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/logs/hmmsearch_out.log
+      contains:
+        - "# hmmsearch :: search profile(s) against a sequence database"
+        - "# target sequence database:"
+        - "Internal pipeline statistics summary:"
+        - "[ok]"
+    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/logs/prodigal_err.log
+      md5sum: c1fdc6977332f53dfe7f632733bb4585
+    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/logs/prodigal_out.log
+      md5sum: 50752acb1c5a20be886bfdfc06635bcb
+    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/prodigal_output/.checkpoint
+      contains:
+        - "Tool: prodigal"
+        - "Completed"
+        - "jobs"
+    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/prodigal_output/predicted_genes/predicted.faa
+      md5sum: 8166471fc5f08c82fd5643ab42327f9d
+    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/prodigal_output/predicted_genes/predicted.fna
+      md5sum: ddc508a18f60e7f3314534df50cdf8ca
+    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11.faa
+      md5sum: 8166471fc5f08c82fd5643ab42327f9d
+    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11.fna
+      md5sum: ddc508a18f60e7f3314534df50cdf8ca
+    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11_err.log
+      md5sum: c1fdc6977332f53dfe7f632733bb4585
+    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11_out.log
+      md5sum: 50752acb1c5a20be886bfdfc06635bcb
+    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_4.faa
+      md5sum: e56fd59c38248dc21ac94355dca98121
+    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_4.fna
+      md5sum: b365f84bf99c68357952e0b98ed7ce42
+    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_4_err.log
+      md5sum: e5f14d7925ba14a0f9850542f3739894
+    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_4_out.log
+      md5sum: d41971bfc1b621d4ffd2633bc47017ea
+    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/run_bacteria_odb10/.bbtools_output/.checkpoint
+      contains:
+        - "Tool: bbtools"
+        - "Completed"
+        - "jobs"
+    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/run_bacteria_odb10/busco_sequences/fragmented_busco_sequences.tar.gz
+    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/run_bacteria_odb10/busco_sequences/multi_copy_busco_sequences.tar.gz
+    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/run_bacteria_odb10/busco_sequences/single_copy_busco_sequences.tar.gz
+    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/run_bacteria_odb10/full_table.tsv
+      md5sum: f473ded1f1db2463533d51be6ed6fd2d
+    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/run_bacteria_odb10/hmmer_output.tar.gz
+    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/run_bacteria_odb10/missing_busco_list.tsv
+      md5sum: 8e6b6a4ba25caf8e7ad15e8a77064755
+    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/run_bacteria_odb10/short_summary.json
+      contains:
+        - "one_line_summary"
+        - "mode"
+        - "dataset"
+    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/run_bacteria_odb10/short_summary.txt
+      contains:
+        - "# BUSCO version is:"
+        - "Results:"
+        - "busco:"
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/logs/bbtools_err.log
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/logs/bbtools_out.log
+      contains:
+        - "IUPAC"
+        - "genome scaffold"
+        - "Coverage"
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/logs/hmmsearch_err.log
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/logs/hmmsearch_out.log
+      contains:
+        - "# hmmsearch :: search profile(s) against a sequence database"
+        - "# target sequence database:"
+        - "Internal pipeline statistics summary:"
+        - "[ok]"
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/logs/prodigal_err.log
+      md5sum: 538510cfc7483498210f01e53fe035ad
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/logs/prodigal_out.log
+      md5sum: 61050b0706addc9498b2088a2d6efa9a
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/.checkpoint
+      contains:
+        - "Tool: prodigal"
+        - "Completed"
+        - "jobs"
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/predicted_genes/predicted.faa
+      md5sum: 836e9a80d33d8b89168f07ddc13ee991
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/predicted_genes/predicted.fna
+      md5sum: 20eeb75f86842e6e136f02bca8b73a9f
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11.faa
+      md5sum: 836e9a80d33d8b89168f07ddc13ee991
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11.fna
+      md5sum: 20eeb75f86842e6e136f02bca8b73a9f
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11_err.log
+      md5sum: 538510cfc7483498210f01e53fe035ad
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11_out.log
+      md5sum: 61050b0706addc9498b2088a2d6efa9a
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/.bbtools_output/.checkpoint
+      contains:
+        - "Tool: bbtools"
+        - "Completed"
+        - "jobs"
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/busco_sequences/fragmented_busco_sequences.tar.gz
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/busco_sequences/multi_copy_busco_sequences.tar.gz
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/busco_sequences/single_copy_busco_sequences.tar.gz
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/full_table.tsv
+      md5sum: 275a7ece09ef61aa59ee7a811289e3d8
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/hmmer_output.tar.gz
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/missing_busco_list.tsv
+      md5sum: ab574cde031a3fbff471976ea61e215d
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/short_summary.json
+      contains:
+        - "one_line_summary"
+        - "mode"
+        - "dataset"
+    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/short_summary.txt
+      contains:
+        - "# BUSCO version is:"
+        - "Results:"
+        - "busco:"
+    - path: output/busco/test-bacteria_odb10-busco/logs/busco.log
+      contains:
+        - "DEBUG:busco.run_BUSCO"
+        - "Results from dataset"
+        - "how to cite BUSCO"
 
 - name: busco test_busco_eukaryote_metaeuk
-  command: nextflow run tests/modules/busco -entry test_busco_eukaryote_metaeuk -c tests/config/nextflow.config
+  command: nextflow run ./tests/modules/busco -entry test_busco_eukaryote_metaeuk -c ./tests/config/nextflow.config  -c ./tests/modules/busco/nextflow.config
   tags:
     - busco
   files:
     - path: output/busco/short_summary.specific.eukaryota_odb10.genome.fasta.json
       contains:
         - "one_line_summary"
-        - "input_file"
         - "mode"
         - "dataset"
     - path: output/busco/short_summary.specific.eukaryota_odb10.genome.fasta.txt
@@ -107,29 +342,132 @@
         - "Missing BUSCOs"
         - "Dependencies and versions"
     - path: output/busco/test-eukaryota_odb10-busco.batch_summary.txt
-      md5sum: a70806f99ba5706d7353d3353b3f1d2b
-    - path: output/busco/versions.yml
-      md5sum: 34a808c257e6db1b0456f3b4372bc477
+      md5sum: ff6d8277e452a83ce9456bbee666feb6
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/bbtools_err.log
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/bbtools_out.log
+      contains:
+        - "IUPAC"
+        - "genome scaffold"
+        - "Coverage"
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/hmmsearch_err.log
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/hmmsearch_out.log
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/metaeuk_run1_err.log
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/metaeuk_run1_out.log
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/metaeuk_run2_err.log
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/metaeuk_run2_out.log
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/.bbtools_output/.checkpoint
+      contains:
+        - "Tool: bbtools"
+        - "Completed"
+        - "jobs"
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/busco_sequences/fragmented_busco_sequences.tar.gz
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/busco_sequences/multi_copy_busco_sequences.tar.gz
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/busco_sequences/single_copy_busco_sequences.tar.gz
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/full_table.tsv
+      md5sum: ff1b64c2adadcf9f0a954a19893e421b
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/hmmer_output.tar.gz
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/metaeuk_output/.checkpoint
+      contains:
+        - "Tool: metaeuk"
+        - "Completed"
+        - "jobs"
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/metaeuk_output/combined_pred_proteins.fas
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/metaeuk_output/initial_results/genome.fasta.codon.fas
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/metaeuk_output/initial_results/genome.fasta.fas
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/metaeuk_output/initial_results/genome.fasta.gff
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/metaeuk_output/initial_results/genome.fasta.headersMap.tsv
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/metaeuk_output/refseq_db_rerun.faa
+      md5sum: d80b8fa4cb5ed0d47d63d6aa93635bc2
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/metaeuk_output/rerun_results/genome.fasta.codon.fas
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/metaeuk_output/rerun_results/genome.fasta.fas
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/metaeuk_output/rerun_results/genome.fasta.gff
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/metaeuk_output/rerun_results/genome.fasta.headersMap.tsv
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/missing_busco_list.tsv
+      md5sum: 6c17c7e06991db898b318b932d686406
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/short_summary.json
+      contains:
+        - "one_line_summary"
+        - "mode"
+        - "dataset"
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/short_summary.txt
+      contains:
+        - "# BUSCO version is:"
+        - "Results:"
+        - "busco:"
+    - path: output/busco/test-eukaryota_odb10-busco/logs/busco.log
+      contains:
+        - "DEBUG:busco.run_BUSCO"
+        - "Results from dataset"
+        - "how to cite BUSCO"
 
 - name: busco test_busco_eukaryote_augustus
-  command: nextflow run tests/modules/busco -entry test_busco_eukaryote_augustus -c tests/config/nextflow.config
+  command: nextflow run ./tests/modules/busco -entry test_busco_eukaryote_augustus -c ./tests/config/nextflow.config  -c ./tests/modules/busco/nextflow.config
   tags:
     - busco
   files:
     - path: output/busco/test-eukaryota_odb10-busco.batch_summary.txt
-      md5sum: 660393dd43cd6a093b952d4b8ad41e40
-    - path: output/busco/versions.yml
-      md5sum: 2caac915461410b16a1524ac064cd0df
+      md5sum: cdd3ffd590a778cdd2f0f367ee86eba7
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/blast_db/.checkpoint
+      contains:
+        - "Tool: makeblastdb"
+        - "Completed"
+        - "jobs"
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/blast_db/genome.fasta.ndb
+      md5sum: 0d553c830656469211de113c5022f06d
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/blast_db/genome.fasta.nhr
+      md5sum: 82396da5130a85faf6d454e2889a1d45
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/blast_db/genome.fasta.nin
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/blast_db/genome.fasta.njs
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/blast_db/genome.fasta.not
+      md5sum: 1e53e9d08f1d23af0299cfa87478a7bb
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/blast_db/genome.fasta.nsq
+      md5sum: 4bc119903ac72152363f47612645046a
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/blast_db/genome.fasta.ntf
+      md5sum: de1250813f0c7affc6d12dac9d0fb6bb
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/blast_db/genome.fasta.nto
+      md5sum: 33cdeccccebe80329f1fdbee7f5874cb
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/bbtools_err.log
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/bbtools_out.log
+      contains:
+        - "IUPAC"
+        - "genome scaffold"
+        - "Coverage"
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/makeblastdb_err.log
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/makeblastdb_out.log
+      contains:
+        - "Building a new DB"
+        - "Adding sequences from FASTA"
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/tblastn_err.log
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/tblastn_out.log
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/.bbtools_output/.checkpoint
+      contains:
+        - "Tool: bbtools"
+        - "Completed"
+        - "jobs"
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/blast_output/.checkpoint
+      contains:
+        - "Tool: tblastn"
+        - "Completed"
+        - "jobs"
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/blast_output/coordinates.tsv
+    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/blast_output/tblastn.tsv
+      contains:
+        - "TBLASTN"
+        - "BLAST processed"
+        - "queries"
+    - path: output/busco/test-eukaryota_odb10-busco/logs/busco.log
+      contains:
+        - "DEBUG:busco.run_BUSCO"
+        - "Running Augustus gene predictor"
 
 - name: busco test_busco_protein
-  command: nextflow run tests/modules/busco -entry test_busco_protein -c tests/config/nextflow.config
+  command: nextflow run ./tests/modules/busco -entry test_busco_protein -c ./tests/config/nextflow.config  -c ./tests/modules/busco/nextflow.config
   tags:
     - busco
   files:
     - path: output/busco/short_summary.specific.bacteria_odb10.proteome.fasta.json
       contains:
         - "one_line_summary"
-        - "input_file"
         - "mode"
         - "dataset"
     - path: output/busco/short_summary.specific.bacteria_odb10.proteome.fasta.txt
@@ -141,19 +479,46 @@
         - "Missing BUSCOs"
         - "Dependencies and versions"
     - path: output/busco/test-bacteria_odb10-busco.batch_summary.txt
-      md5sum: fd3b4e30ce74d1fcb95d6286d6e2049f
-    - path: output/busco/versions.yml
-      md5sum: d7392261a57960a7e6aea609dce824f5
+      md5sum: 7a65e6cbb6c56a2ea4e739ae0aa3297d
+    - path: output/busco/test-bacteria_odb10-busco/logs/busco.log
+      contains:
+        - "DEBUG:busco.run_BUSCO"
+        - "Results from dataset"
+        - "how to cite BUSCO"
+    - path: output/busco/test-bacteria_odb10-busco/proteome.fasta/logs/hmmsearch_err.log
+    - path: output/busco/test-bacteria_odb10-busco/proteome.fasta/logs/hmmsearch_out.log
+      contains:
+        - "# hmmsearch :: search profile(s) against a sequence database"
+        - "# target sequence database:"
+        - "Internal pipeline statistics summary:"
+        - "[ok]"
+    - path: output/busco/test-bacteria_odb10-busco/proteome.fasta/run_bacteria_odb10/busco_sequences/fragmented_busco_sequences.tar.gz
+    - path: output/busco/test-bacteria_odb10-busco/proteome.fasta/run_bacteria_odb10/busco_sequences/multi_copy_busco_sequences.tar.gz
+    - path: output/busco/test-bacteria_odb10-busco/proteome.fasta/run_bacteria_odb10/busco_sequences/single_copy_busco_sequences.tar.gz
+    - path: output/busco/test-bacteria_odb10-busco/proteome.fasta/run_bacteria_odb10/full_table.tsv
+      md5sum: 81e0e9a5897bb72fffbb1866779f6834
+    - path: output/busco/test-bacteria_odb10-busco/proteome.fasta/run_bacteria_odb10/hmmer_output.tar.gz
+    - path: output/busco/test-bacteria_odb10-busco/proteome.fasta/run_bacteria_odb10/missing_busco_list.tsv
+      md5sum: 8e6b6a4ba25caf8e7ad15e8a77064755
+    - path: output/busco/test-bacteria_odb10-busco/proteome.fasta/run_bacteria_odb10/short_summary.json
+      contains:
+        - "one_line_summary"
+        - "mode"
+        - "dataset"
+    - path: output/busco/test-bacteria_odb10-busco/proteome.fasta/run_bacteria_odb10/short_summary.txt
+      contains:
+        - "# BUSCO version is:"
+        - "Results:"
+        - "busco:"
 
 - name: busco test_busco_transcriptome
-  command: nextflow run tests/modules/busco -entry test_busco_transcriptome -c tests/config/nextflow.config
+  command: nextflow run ./tests/modules/busco -entry test_busco_transcriptome -c ./tests/config/nextflow.config  -c ./tests/modules/busco/nextflow.config
   tags:
     - busco
   files:
     - path: output/busco/short_summary.specific.bacteria_odb10.test1.contigs.fa.json
       contains:
         - "one_line_summary"
-        - "input_file"
         - "mode"
         - "dataset"
     - path: output/busco/short_summary.specific.bacteria_odb10.test1.contigs.fa.txt
@@ -165,6 +530,158 @@
         - "Missing BUSCOs"
         - "Dependencies and versions"
     - path: output/busco/test-bacteria_odb10-busco.batch_summary.txt
-      md5sum: 9a176cafe66ac0adca89dc34ad2be13f
-    - path: output/busco/versions.yml
-      md5sum: 30eacbc7df70f6b1e72e0a7b6d02a7e1
+      md5sum: 46118ecf60d1b87d22b96d80f4f03632
+    - path: output/busco/test-bacteria_odb10-busco/logs/busco.log
+      contains:
+        - "DEBUG:busco.run_BUSCO"
+        - "Results from dataset"
+        - "how to cite BUSCO"
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/blast_db/.checkpoint
+      contains:
+        - "Tool: makeblastdb"
+        - "Completed"
+        - "jobs"
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/blast_db/test1.contigs.fa.ndb
+      md5sum: 3788c017fe5e6f0f58224e9cdd21822b
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/blast_db/test1.contigs.fa.nhr
+      md5sum: 8ecd2ce392bb5e25ddbe1d85f879582e
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/blast_db/test1.contigs.fa.nin
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/blast_db/test1.contigs.fa.njs
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/blast_db/test1.contigs.fa.not
+      md5sum: 0c340e376c7e85d19f82ec1a833e6a6e
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/blast_db/test1.contigs.fa.nsq
+      md5sum: 532d5c0a7ea00fe95ca3c97cb3be6198
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/blast_db/test1.contigs.fa.ntf
+      md5sum: de1250813f0c7affc6d12dac9d0fb6bb
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/blast_db/test1.contigs.fa.nto
+      md5sum: ff74bd41f9cc9b011c63a32c4f7693bf
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/logs/hmmsearch_err.log
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/logs/hmmsearch_out.log
+      contains:
+        - "# hmmsearch :: search profile(s) against a sequence database"
+        - "# target sequence database:"
+        - "Internal pipeline statistics summary:"
+        - "[ok]"
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/logs/makeblastdb_err.log
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/logs/makeblastdb_out.log
+      contains:
+        - "Building a new DB"
+        - "Adding sequences from FASTA"
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/logs/tblastn_err.log
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/logs/tblastn_out.log
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/.checkpoint
+      contains:
+        - "Tool: tblastn"
+        - "Completed"
+        - "jobs"
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/coordinates.tsv
+      md5sum: cc30eed321944af293452bdbcfc24292
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_101.temp
+      md5sum: 73e9c65fc83fedc58f57f09b08f08238
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_119.temp
+      md5sum: 7fa4cc7955ec0cc36330a221c579b975
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_129.temp
+      md5sum: 6f1601c875d019e3f6f1f98ed8e988d4
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_138.temp
+      md5sum: 3f8e034686cd240c2330650d791bcae2
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_143.temp
+      md5sum: df3dfa8e9ba30ed70cf75b5e7abf2179
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_172.temp
+      md5sum: 7d463e0e6cf7169bc9077d8dc776dda1
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_178.temp
+      md5sum: 2288edf7fa4f88f51b4cf4d94086f77e
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_188.temp
+      md5sum: 029906abbad6d87fc57830dd548cac24
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_195.temp
+      md5sum: 4937f3b348774a31b1160a00297c29cc
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_210.temp
+      md5sum: afcb20ba4c466479d6b91c8c62251e1f
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_232.temp
+      md5sum: 2e1e823ce017345bd998191a39fa9924
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_268.temp
+      md5sum: 08c2d82c34ecffbe1c638b410349412e
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_29.temp
+      md5sum: cd9b63cf93524284781535c888313764
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_44.temp
+      md5sum: d1929b742b24ebe379bf4801ca882dca
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_58.temp
+      md5sum: 69215765b010c05336538cb322c900b3
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_72.temp
+      md5sum: 6feaa1cc3b0899a147ea9d466878f3e3
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_80.temp
+      md5sum: 13625eae14e860a96ce17cd4e37e9d01
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_81.temp
+      md5sum: e14b2484649b0dbc8926815c207b806d
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_93.temp
+      md5sum: 6902c93691df00e690faea914c71839e
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_97.temp
+      md5sum: 0a0d9d38a83acbd5ad43c29cdf429988
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/tblastn.tsv
+      contains:
+        - "TBLASTN"
+        - "BLAST processed"
+        - "queries"
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/busco_sequences/fragmented_busco_sequences.tar.gz
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/busco_sequences/multi_copy_busco_sequences.tar.gz
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/busco_sequences/single_copy_busco_sequences.tar.gz
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/full_table.tsv
+      md5sum: 14bb2d7788bd0aa547e4a99df6659f1e
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/hmmer_output.tar.gz
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/missing_busco_list.tsv
+      md5sum: 485902b7b62403985ee9f781e17b20ab
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/short_summary.json
+      contains:
+        - "one_line_summary"
+        - "mode"
+        - "dataset"
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/short_summary.txt
+      contains:
+        - "# BUSCO version is:"
+        - "Results:"
+        - "busco:"
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/single_copy_proteins.faa
+      md5sum: e04b9465733577ae6e4bccb7aa01e720
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/1024388at2.faa
+      md5sum: 7333c39a20258f20c7019ea0cd83157c
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/1054741at2.faa
+      md5sum: ebb481e77a824685fbe04d8a2f3a0d7d
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/1093223at2.faa
+      md5sum: 34621c7d499034e8f8e6b92fd4020a93
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/1151822at2.faa
+      md5sum: aa89ca381c1c70c9c4e1380351ca7c2a
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/143460at2.faa
+      md5sum: f2e91d78b8dd3722840378789f29e8c8
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/1491686at2.faa
+      md5sum: 73c25aef5c9cba7f4151804941b146ea
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/1504821at2.faa
+      md5sum: cda556018d1f84ebe517e89f6fc107d0
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/1574817at2.faa
+      md5sum: a9096c9fb8b25c78a72871ab0463acdc
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/1592033at2.faa
+      md5sum: e463d25ce186c0cebfd749474f3a4c64
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/1623045at2.faa
+      md5sum: f2cfd241590c6d8377286d6135480937
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/1661836at2.faa
+      md5sum: 586569546fb9861502468e3d9ba2775c
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/1674344at2.faa
+      md5sum: 24c658bee14ad84b062d81ad96642eb8
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/1698718at2.faa
+      md5sum: 0b8e26ddf5149bbd8805be7af125208d
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/1990650at2.faa
+      md5sum: 159320712ee01fb2ccb31a25df44eead
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/223233at2.faa
+      md5sum: 812629c0b06ac3d18661c2ca78de0c08
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/402899at2.faa
+      md5sum: f7ff4e1591342d30b77392a2e84b57d9
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/505485at2.faa
+      md5sum: 7b34a24fc49c540d46fcf96ff5129564
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/665824at2.faa
+      md5sum: 4cff2df64f6bcaff8bc19c234c8bcccd
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/776861at2.faa
+      md5sum: 613af7a3fea30ea2bece66f603b9284a
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/874197at2.faa
+      md5sum: a7cd1b13c9ef91c7ef4e31614166f197
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/932854at2.faa
+      md5sum: fe313ffd5efdb0fed887a04fba352552
+    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/95696at2.faa
+      md5sum: 4e1f30a2fea4dfbf9bb7fae2700622a0