Add stub and update test

conf/test.config

@@ -10,6 +10,8 @@
 ----------------------------------------------------------------------------------------
 */
 
+stubRun = true
+
 params {
     config_profile_name        = 'Test profile'
     config_profile_description = 'Minimal test dataset to check pipeline function'
@@ -29,3 +31,4 @@ params {
     skip_iqtree      = true
     fastme_bootstrap = 0
 }
+

modules/local/convert_fasta.nf

@@ -28,4 +28,16 @@ process CONVERT_FASTA {
         Biopython: \$(pip show biopython | grep Version | cut -d ' ' -f 2)
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.fa
+
+    cat <<- END_VERSIONS > versions.yml
+    "${task.process}":
+        Python: \$(python --version | cut -d ' ' -f 2)
+        Biopython: \$(pip show biopython | grep Version | cut -d ' ' -f 2)
+    END_VERSIONS
+    """
 }

modules/local/convert_phylip.nf

@@ -28,4 +28,16 @@ process CONVERT_PHYLIP {
         Biopython: \$(pip show biopython | grep Version | cut -d ' ' -f 2)
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.phy
+
+    cat <<- END_VERSIONS > versions.yml
+    "${task.process}":
+        Python: \$(python --version | cut -d ' ' -f 2)
+        Biopython: \$(pip show biopython | grep Version | cut -d ' ' -f 2)
+    END_VERSIONS
+    """
 }

modules/local/create_tcoffeetemplate.nf

@@ -20,7 +20,10 @@ process CREATE_TCOFFEETEMPLATE {
     prefix   = task.ext.prefix ?: "${meta.id}"
     """
     # Prep templates
-    for structure in \$(ls *.pdb); do id=`echo \$structure| awk  {'gsub(".pdb", "", \$0); print'}`; echo -e ">"\$id "_P_" "\${id}" >>${prefix}_template.txt ; done
+    for structure in \$(ls *.pdb); do
+        id=`echo \$structure | awk  {'gsub(".pdb", "", \$0); print'}`;
+        echo -e ">"\$id "_P_" "\${id}" >> ${prefix}_template.txt; 
+    done
     """
 
     stub:

modules/local/dump_params.nf

@@ -8,6 +8,13 @@ process DUMP_PARAMS {
 
     input:
     tuple val(meta), path(exact)
+    val uniprot_query
+    val use_structures
+    val use_centroid
+    val min_score
+    val skip_downstream
+    val use_iqtree
+    val use_fastme
 
     output:
     tuple val(meta), path("params.yml"), emit: params
@@ -19,14 +26,19 @@ process DUMP_PARAMS {
     """
     cat <<- END_PARAMS > params.yml
     id: ${meta.id}
-    uniprot_query: ${params.uniprot_query}
+    uniprot_query: ${uniprot_query}
     exact_match: \$(cat $exact)
-    use_structures: ${params.use_structures}
-    use_centroid: ${params.use_centroid}
-    min_score: ${params.min_score}
-    skip_downstream: ${params.skip_downstream}
-    use_iqtree: ${params.use_iqtree}
-    use_fastme: ${params.use_fastme}
+    use_structures: ${use_structures}
+    use_centroid: ${use_centroid}
+    min_score: ${min_score}
+    skip_downstream: ${skip_downstream}
+    use_iqtree: ${use_iqtree}
+    use_fastme: ${use_fastme}
     END_PARAMS
     """
+
+    stub:
+    """
+    touch params.yml
+    """
 }

modules/local/fetch_afdb_structures.nf

@@ -31,4 +31,16 @@ process FETCH_AFDB_STRUCTURES {
         Python Requests: \$(pip show requests | grep Version | cut -d ' ' -f 2)
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.phy
+
+    cat <<- END_VERSIONS > versions.yml
+    "${task.process}"
+        Python: \$(python --version | cut -d ' ' -f 2)
+        Python Requests: \$(pip show requests | grep Version | cut -d ' ' -f 2)
+    END_VERSIONS
+    """
 }

modules/local/fetch_eggnog_group_local.nf

@@ -2,6 +2,11 @@ process FETCH_EGGNOG_GROUP_LOCAL {
     tag "$meta.id"
     label 'process_single'
 
+    conda "conda-forge::python=3.11.0 conda-forge::biopython=1.83.0 conda-forge::requests=2.31.0"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' :
+        'biocontainers/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' }"
+
     conda "conda-forge::python=3.11.0 conda-forge::biopython=1.83.0 conda-forge::requests=2.31.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' :
@@ -32,5 +37,16 @@ process FETCH_EGGNOG_GROUP_LOCAL {
         Python: \$(python --version | cut -f2)
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_eggnog_group.txt
+    touch ${prefix}_eggnog_group.csv
 
+    cat <<- END_VERSIONS > versions.yml
+    "${task.process}":
+        Python: \$(python --version | cut -f2)
+    END_VERSIONS
+    """
 }

modules/local/fetch_inspector_group_online.nf

@@ -32,4 +32,17 @@ process FETCH_INSPECTOR_GROUP_ONLINE {
         OrthoInspector Database: $inspector_version
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_inspector_group.csv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        Python: \$(python --version | cut -d ' ' -f 2)
+        Python Requests: \$(pip show requests | grep Version | cut -d ' ' -f 2)
+        OrthoInspector Database: $inspector_version
+    END_VERSIONS
+    """
 }

modules/local/fetch_oma_group_local.nf

@@ -2,6 +2,11 @@ process FETCH_OMA_GROUP_LOCAL {
     tag "$meta.id"
     label 'process_single'
 
+    conda "conda-forge::python=3.11.0 conda-forge::biopython=1.83.0 conda-forge::requests=2.31.0"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' :
+        'biocontainers/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' }"
+
     conda "conda-forge::python=3.11.0 conda-forge::biopython=1.83.0 conda-forge::requests=2.31.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' :
@@ -36,4 +41,14 @@ process FETCH_OMA_GROUP_LOCAL {
     END_VERSIONS
     """
 
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_oma_group.csv
+
+    cat <<- END_VERSIONS > versions.yml
+    "${task.process}":
+        Python: \$(python --version | cut -f2)
+    END_VERSIONS
+    """
 }

modules/local/fetch_oma_group_online.nf

@@ -33,4 +33,17 @@ process FETCH_OMA_GROUP_ONLINE {
     \$(get_oma_version.py)
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_oma_group.csv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        Python: \$(python --version | cut -d ' ' -f 2)
+        Python Requests: \$(pip show requests | grep Version | cut -d ' ' -f 2)
+    \$(get_oma_version.py)
+    END_VERSIONS
+    """
 }

modules/local/fetch_panther_group_local.nf

@@ -7,6 +7,11 @@ process FETCH_PANTHER_GROUP_LOCAL {
         'https://depot.galaxyproject.org/singularity/python:3.10' :
         'biocontainers/python:3.10' }"
 
+    conda "conda-forge::python=3.11.0 conda-forge::biopython=1.83.0 conda-forge::requests=2.31.0"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' :
+        'biocontainers/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' }"
+
     input:
     tuple val(meta), path(uniprot_id), path(taxid), path(exact)
     path panther_db
@@ -30,4 +35,15 @@ process FETCH_PANTHER_GROUP_LOCAL {
         Python: \$(python --version | cut -f2)
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_panther_group.csv
+
+    cat <<- END_VERSIONS > versions.yml
+    "${task.process}":
+        Python: \$(python --version | cut -f2)
+    END_VERSIONS
+    """
 }

modules/local/fetch_panther_group_online.nf

@@ -32,4 +32,17 @@ process FETCH_PANTHER_GROUP_ONLINE {
         Panther Database: \$(cat panther_version.txt)
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_panther_group.csv
+
+    cat <<- END_VERSIONS > versions.yml
+    "${task.process}":
+        Python: \$(python --version | cut -d ' ' -f 2)
+        Python Requests: \$(pip show requests | grep Version | cut -d ' ' -f 2)
+        Panther Database: \$(cat panther_version.txt)
+    END_VERSIONS
+    """
 }

modules/local/fetch_sequences_online.nf

@@ -33,4 +33,19 @@ process FETCH_SEQUENCES_ONLINE {
     \$(get_oma_version.py)
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_orthologs.fa
+    touch ${prefix}_seq_hits.txt
+    touch ${prefix}_seq_misses.txt
+
+    cat <<- END_VERSIONS > versions.yml
+    "${task.process}":
+        Python: \$(python --version | cut -d ' ' -f 2)
+        Python Requests: \$(pip show requests | grep Version | cut -d ' ' -f 2)
+    \$(get_oma_version.py)
+    END_VERSIONS
+    """
 }

modules/local/filter_fasta.nf

@@ -2,6 +2,11 @@ process FILTER_FASTA {
     tag "$meta.id"
     label 'process_single'
 
+    conda "conda-forge::python=3.11.0 conda-forge::biopython=1.83.0 conda-forge::requests=2.31.0"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' :
+        'biocontainers/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' }"
+
     conda "conda-forge::python=3.11.0 conda-forge::biopython=1.83.0 conda-forge::requests=2.31.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' :
@@ -27,4 +32,15 @@ process FILTER_FASTA {
         Python: \$(python --version | cut -d ' ' -f 2)
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_filtered.fa
+
+    cat <<- END_VERSIONS > versions.yml
+    "${task.process}":
+        Python: \$(python --version | cut -f2)
+    END_VERSIONS
+    """
 }

modules/local/filter_hits.nf

@@ -32,4 +32,17 @@ process FILTER_HITS {
         Python: \$(python --version | cut -d ' ' -f 2)
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_minscore_000.txt
+    touch ${prefix}_centroid.txt
+    touch ${prefix}_filtered_hits.txt
+
+    cat <<- END_VERSIONS > versions.yml
+    "${task.process}":
+        Python: \$(python --version | cut -f2)
+    END_VERSIONS
+    """
 }

modules/local/identify_seq_online.nf

@@ -29,4 +29,18 @@ process IDENTIFY_SEQ_ONLINE {
         Python Requests: \$(pip show requests | grep Version | cut -d ' ' -f 2)
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_id.txt
+    touch ${prefix}_taxid.txt
+    touch ${prefix}_exact.txt
+
+    cat <<- END_VERSIONS > versions.yml
+    "${task.process}":
+        Python: \$(python --version | cut -d ' ' -f 2)
+        Python Requests: \$(pip show requests | grep Version | cut -d ' ' -f 2)
+    END_VERSIONS
+    """
 }

modules/local/make_report.nf

@@ -6,7 +6,6 @@ process MAKE_REPORT {
         'docker://itrujnara/orthologs-report:1.0.0' :
         'itrujnara/orthologs-report:1.0.0' }"
 
-
     input:
     tuple val(meta), path(id), path(taxid), path(exact), path(score_table), path(filtered_hits), path(support_plot), path(venn_plot), path(jaccard_plot), path(orthostats), path(seq_hits), path(seq_misses), path(str_hits), path(str_misses), path(alignment), path(iqtree), path(fastme), path(params_file)
 
@@ -59,4 +58,19 @@ process MAKE_REPORT {
         Python: \$(python --version | cut -d ' ' -f 2)
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    mkdir ${prefix}_dist
+    touch ${prefix}_dist/${prefix}_run.sh
+
+    cat <<- END_VERSIONS > versions.yml
+    ${task.process}:
+        Node: \$(node --version)
+        Yarn: \$(yarn --version)
+        React: \$(yarn view react version)
+        Python: \$(python --version | cut -d ' ' -f 2)
+    END_VERSIONS
+    """
 }

modules/local/make_score_table.nf

@@ -27,4 +27,15 @@ process MAKE_SCORE_TABLE {
         Python: \$(python3 --version | cut -d ' ' -f 2)
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_score_table.csv
+
+    cat <<- END_VERSIONS > versions.yml
+    "${task.process}":
+        Python: \$(python3 --version | cut -d ' ' -f 2)
+    END_VERSIONS
+    """
 }