Added a test for invalid files

Plant-Food-Research-Open · Feb 28, 2024 · cb325c0 · cb325c0
1 parent 1321d59
commit cb325c0
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -25,10 +25,10 @@ jobs:
       matrix:
         NXF_VER:
           - "23.04.0"
-          - "latest-everything"
         RUN_CONFIG:
           - "-profile test,docker"
           - "-profile docker -c ./tests/stub/stub.config -stub"
+          - "-profile docker -params-file ./tests/invalid/params.json"
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v4

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## v1.4dev - [20-Feb-2024]
+## v1.4dev - [28-Feb-2024]
 
 ### `Added`
 
@@ -24,6 +24,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 15. Refactored and cleaned data flows for all the custom sub-workflow
 16. Started using nf-core template
 17. Started using semantic versioning
+18. Moved all python depending packages to 'docker.io/gallvp/python3npkgs:v0.6'
 
 ### `Fixed`
 

diff --git a/bin/report_modules/templates/base.html b/bin/report_modules/templates/base.html
@@ -1,68 +1,57 @@
 <html>
-    {% include 'header.html' %}
+{% include 'header.html' %}
+
+<body>
+  <div class="report-header-wrapper">
+    <div class="report-header">AssemblyQC {{
+      all_stats_dicts['VERSIONS']['Workflow']['plant-food-research-open/assemblyqc'] }}</div>
+  </div>
+  <div class="tab" id="topNavBarButtons">
+    <button class="tablinks active" onclick="openTool(event, 'PARAMS')">PARAMS</button>
+    <button class="tablinks active" onclick="openTool(event, 'TOOLS')">TOOLS</button>
+    {% if 'FASTA_VALIDATE' in all_stats_dicts %}
+    <button class="tablinks active" onclick="openTool(event, 'FASTA_VALIDATE')">FASTA VALIDATE</button>
+    {% endif %}
+    {% if 'GFF3_VALIDATE' in all_stats_dicts %}
+    <button class="tablinks active" onclick="openTool(event, 'GFF3_VALIDATE')">GFF3 VALIDATE</button>
+    {% endif %}
+    {% if 'NCBI_FCS_ADAPTOR' in all_stats_dicts %}
+    <button class="tablinks active" onclick="openTool(event, 'NCBI_FCS_ADAPTOR')">NCBI FCS ADAPTOR</button>
+    {% endif %} {% if 'NCBI_FCS_GX' in all_stats_dicts %}<button class="tablinks"
+      onclick="openTool(event, 'NCBI_FCS_GX')">
+      NCBI FCS GX</button>{% endif %} {% if 'ASSEMBLATHON_STATS' in all_stats_dicts %}<button class="tablinks active"
+      onclick="openTool(event, 'ASSEMBLATHON_STATS')">
+      ASSEMBLATHON STATS</button>{% endif %} {% if 'GENOMETOOLS_GT_STAT' in all_stats_dicts %}<button
+      class="tablinks active" onclick="openTool(event, 'GENOMETOOLS_GT_STAT')">
+      GENOMETOOLS GT STAT</button>{% endif %} {% if 'BUSCO' in all_stats_dicts %}<button class="tablinks active"
+      onclick="openTool(event, 'BUSCO')">
+      BUSCO</button>{% endif %} {% if 'TIDK' in all_stats_dicts %}<button class="tablinks"
+      onclick="openTool(event, 'TIDK')">
+      TIDK</button>{% endif %} {% if 'LAI' in all_stats_dicts %}<button class="tablinks"
+      onclick="openTool(event, 'LAI')">
+      LAI</button>{% endif %} {% if 'KRAKEN2' in all_stats_dicts %}<button class="tablinks"
+      onclick="openTool(event, 'KRAKEN2')">
+      KRAKEN2</button>{% endif %} {% if 'HIC' in all_stats_dicts %}<button class="tablinks"
+      onclick="openTool(event, 'HIC')">
+      HIC</button>{% endif %} {% if 'CIRCOS' in all_stats_dicts %}<button class="tablinks"
+      onclick="openTool(event, 'CIRCOS')">
+      CIRCOS</button>{% endif %}
+  </div>
+  {% include 'params/params.html' %} {% include 'tools/tools.html' %} {% if 'FASTA_VALIDATE' in all_stats_dicts %}{%
+  include 'fasta_validate/fasta_validate.html' %}{% endif %}
+
+  {% if 'GFF3_VALIDATE' in all_stats_dicts %}{% include 'gff3_validate/gff3_validate.html' %}{% endif %}
+
+  {% if 'NCBI_FCS_ADAPTOR' in all_stats_dicts %}{%
+  include 'ncbi_fcs_adaptor/ncbi_fcs_adaptor.html' %}{% endif %} {% if 'NCBI_FCS_GX' in all_stats_dicts %}{%
+  include 'ncbi_fcs_gx/ncbi_fcs_gx.html' %}{% endif %} {% if 'ASSEMBLATHON_STATS' in all_stats_dicts %}{% include
+  'assemblathon_stats/assemblathon_stats.html' %}{% endif %} {% if 'GENOMETOOLS_GT_STAT' in all_stats_dicts %}{%
+  include 'genometools_gt_stat/genometools_gt_stat.html' %}{% endif %} {% if 'BUSCO' in all_stats_dicts %}{%
+  include 'busco/busco.html' %}{% endif %} {% if 'TIDK' in all_stats_dicts %}{% include 'tidk/tidk.html' %}{%
+  endif %} {% if 'LAI' in all_stats_dicts %}{% include 'lai/lai.html' %}{% endif %} {% if 'KRAKEN2' in
+  all_stats_dicts %}{% include 'kraken2/kraken2.html' %}{% endif %} {% if 'HIC' in all_stats_dicts %}{% include
+  'hic/hic.html' %}{% endif %} {% if 'CIRCOS' in all_stats_dicts %}{% include 'circos/circos.html' %}{% endif %}
+</body>
+{% include 'js.html' %}
 
-    <body>
-        <div class="report-header-wrapper">
-            <div class="report-header">AssemblyQC {{ all_stats_dicts['VERSIONS']['Workflow']['plant-food-research-open/assemblyqc'] }}</div>
-        </div>
-        <div class="tab" id="topNavBarButtons">
-            <button class="tablinks active" onclick="openTool(event, 'PARAMS')">PARAMS</button>
-            <button class="tablinks active" onclick="openTool(event, 'TOOLS')">TOOLS</button>
-            {% if 'GFF3_VALIDATE' in all_stats_dicts %}
-            <button class="tablinks active" onclick="openTool(event, 'GFF3_VALIDATE')">GFF3 VALIDATE</button>
-            {% endif %} {% if 'FASTA_VALIDATE' in all_stats_dicts %}
-            <button class="tablinks active" onclick="openTool(event, 'FASTA_VALIDATE')">FASTA VALIDATE</button>
-            {% endif %} {% if 'NCBI_FCS_ADAPTOR' in all_stats_dicts %}
-            <button class="tablinks active" onclick="openTool(event, 'NCBI_FCS_ADAPTOR')">NCBI FCS ADAPTOR</button>
-            {% endif %} {% if 'NCBI_FCS_GX' in all_stats_dicts %}<button
-                class="tablinks"
-                onclick="openTool(event, 'NCBI_FCS_GX')"
-            >
-                NCBI FCS GX</button
-            >{% endif %} {% if 'ASSEMBLATHON_STATS' in all_stats_dicts %}<button
-                class="tablinks active"
-                onclick="openTool(event, 'ASSEMBLATHON_STATS')"
-            >
-                ASSEMBLATHON STATS</button
-            >{% endif %} {% if 'GENOMETOOLS_GT_STAT' in all_stats_dicts %}<button
-                class="tablinks active"
-                onclick="openTool(event, 'GENOMETOOLS_GT_STAT')"
-            >
-                GENOMETOOLS GT STAT</button
-            >{% endif %} {% if 'BUSCO' in all_stats_dicts %}<button
-                class="tablinks active"
-                onclick="openTool(event, 'BUSCO')"
-            >
-                BUSCO</button
-            >{% endif %} {% if 'TIDK' in all_stats_dicts %}<button class="tablinks" onclick="openTool(event, 'TIDK')">
-                TIDK</button
-            >{% endif %} {% if 'LAI' in all_stats_dicts %}<button class="tablinks" onclick="openTool(event, 'LAI')">
-                LAI</button
-            >{% endif %} {% if 'KRAKEN2' in all_stats_dicts %}<button
-                class="tablinks"
-                onclick="openTool(event, 'KRAKEN2')"
-            >
-                KRAKEN2</button
-            >{% endif %} {% if 'HIC' in all_stats_dicts %}<button class="tablinks" onclick="openTool(event, 'HIC')">
-                HIC</button
-            >{% endif %} {% if 'CIRCOS' in all_stats_dicts %}<button
-                class="tablinks"
-                onclick="openTool(event, 'CIRCOS')"
-            >
-                CIRCOS</button
-            >{% endif %}
-        </div>
-        {% include 'params/params.html' %} {% include 'tools/tools.html' %} {% if 'GFF3_VALIDATE' in all_stats_dicts
-        %}{% include 'gff3_validate/gff3_validate.html' %}{% endif %} {% if 'FASTA_VALIDATE' in all_stats_dicts %}{%
-        include 'fasta_validate/fasta_validate.html' %}{% endif %} {% if 'NCBI_FCS_ADAPTOR' in all_stats_dicts %}{%
-        include 'ncbi_fcs_adaptor/ncbi_fcs_adaptor.html' %}{% endif %} {% if 'NCBI_FCS_GX' in all_stats_dicts %}{%
-        include 'ncbi_fcs_gx/ncbi_fcs_gx.html' %}{% endif %} {% if 'ASSEMBLATHON_STATS' in all_stats_dicts %}{% include
-        'assemblathon_stats/assemblathon_stats.html' %}{% endif %} {% if 'GENOMETOOLS_GT_STAT' in all_stats_dicts %}{%
-        include 'genometools_gt_stat/genometools_gt_stat.html' %}{% endif %} {% if 'BUSCO' in all_stats_dicts %}{%
-        include 'busco/busco.html' %}{% endif %} {% if 'TIDK' in all_stats_dicts %}{% include 'tidk/tidk.html' %}{%
-        endif %} {% if 'LAI' in all_stats_dicts %}{% include 'lai/lai.html' %}{% endif %} {% if 'KRAKEN2' in
-        all_stats_dicts %}{% include 'kraken2/kraken2.html' %}{% endif %} {% if 'HIC' in all_stats_dicts %}{% include
-        'hic/hic.html' %}{% endif %} {% if 'CIRCOS' in all_stats_dicts %}{% include 'circos/circos.html' %}{% endif %}
-    </body>
-    {% include 'js.html' %}
 </html>
diff --git a/modules/local/assembly2bedpe.nf b/modules/local/assembly2bedpe.nf
@@ -2,7 +2,7 @@ process ASSEMBLY2BEDPE {
     tag "$sample_id_on_tag"
     label 'process_single'
 
-    container "docker.io/gallvp/python3npkgs:v0.4"
+    container "docker.io/gallvp/python3npkgs:v0.6"
 
     input:
     tuple val(sample_id_on_tag), path(agp_assembly_file)

diff --git a/modules/local/colourbundlelinks.nf b/modules/local/colourbundlelinks.nf
@@ -2,7 +2,7 @@ process COLOURBUNDLELINKS {
     tag "${target_on_ref}"
     label 'process_single'
 
-    container "docker.io/gallvp/python3npkgs:v0.4"
+    container "docker.io/gallvp/python3npkgs:v0.6"
 
     input:
     tuple val(target_on_ref), path(bundle_links)

diff --git a/modules/local/hic2html.nf b/modules/local/hic2html.nf
@@ -2,7 +2,7 @@ process HIC2HTML {
     tag "$sample_id_on_tag"
     label 'process_single'
 
-    container "docker.io/gallvp/python3npkgs:v0.4"
+    container "docker.io/gallvp/python3npkgs:v0.6"
 
     input:
     tuple val(sample_id_on_tag), path(hic_file)

diff --git a/modules/local/relabelbundlelinks.nf b/modules/local/relabelbundlelinks.nf
@@ -2,7 +2,7 @@ process RELABELBUNDLELINKS {
     tag "${target_on_ref}"
     label 'process_single'
 
-    container "docker.io/gallvp/python3npkgs:v0.4"
+    container "docker.io/gallvp/python3npkgs:v0.6"
 
     input:
     tuple val(target_on_ref), path(coloured_bundle_links), path(target_seq_list), path(ref_seq_list)

diff --git a/modules/local/relabelfastalength.nf b/modules/local/relabelfastalength.nf
@@ -2,7 +2,7 @@ process RELABELFASTALENGTH {
     tag "${target_on_ref}"
     label 'process_single'
 
-    container "docker.io/gallvp/python3npkgs:v0.4"
+    container "docker.io/gallvp/python3npkgs:v0.6"
 
     input:
     tuple val(target_on_ref), path(target_seq_lengths), path(ref_seq_lengths), path(target_seq_list), path(ref_seq_list)

diff --git a/tests/invalid/assemblysheet.csv b/tests/invalid/assemblysheet.csv
@@ -0,0 +1,4 @@
+tag,fasta,gff3,monoploid_ids,synteny_labels
+FI1,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/003/814/445/GCA_003814445.1_ASM381444v1/GCA_003814445.1_ASM381444v1_genomic.fna.gz,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/003/814/445/GCA_003814445.1_ASM381444v1/GCA_003814445.1_ASM381444v1_genomic.gff.gz,,
+TT_2021a,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/021/950/295/GCA_021950295.1_ASM2195029v1/GCA_021950295.1_ASM2195029v1_genomic.fna.gz,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/003/814/445/GCA_003814445.1_ASM381444v1/GCA_003814445.1_ASM381444v1_genomic.gff.gz,,
+MISC,tests/invalid/invalid.fsa.gz,,,
diff --git a/tests/invalid/invalid.fsa.gz b/tests/invalid/invalid.fsa.gz
diff --git a/tests/invalid/params.json b/tests/invalid/params.json
@@ -0,0 +1,8 @@
+{
+    "config_profile_name": "Invalid profile",
+    "config_profile_description": "Profile to test invalid files",
+    "input": "tests/invalid/assemblysheet.csv",
+    "max_cpus": 2,
+    "max_memory": "6.GB",
+    "max_time": "6.h"
+}