add modules

modules/local/f5c_index_eventalign.nf

@@ -0,0 +1,32 @@
+process F5C_INDEX_EVENTALIGN {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "bioconda::nanopolish==0.13.2"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/f5c:1.5--h56e2c18_1' :
+        'quay.io/biocontainers/f5c:1.5--h56e2c18_1' }"
+
+    input:
+    tuple val(meta), path(genome), path(gtf), path(fastq), path(bam), path(bai), path(blow5)
+
+    output:
+    tuple val(meta), path(genome), path(gtf), path("*eventalign.txt"), path("*summary.txt"), emit: f5c_outputs
+    path "versions.yml"                                                                    , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    sample_summary = "$meta.id" +"_summary.txt"
+    sample_eventalign = "$meta.id" +"_eventalign.txt"
+    """
+    f5c index --slow5 $blow5 $fastq
+    f5c eventalign  --reads $fastq --bam $bam --genome $genome --slow5 $blow5 --scale-events --signal-index --summary $sample_summary --threads $task.cpus > $sample_eventalign
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        nanopolish: \$( f5c -V | tail -c 4)
+    END_VERSIONS
+    """
+}

modules/local/slow5tools_f2s_merge.nf

@@ -0,0 +1,30 @@
+process SLOW5_F2S_MERGE {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "bioconda::slow5tools==1.2.0"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/slow5tools:1.2.0--h56e2c18_1' :
+        'quay.io/biocontainers/slow5tools:1.2.0--h56e2c18_1' }"
+
+    input:
+    tuple val(meta), path(genome), path(gtf), path(fastq), path(bam), path(bai)
+
+    output:
+    tuple val(meta), path(genome), path(gtf), path("*eventalign.txt"), path("*summary.txt"), emit: nanopolish_outputs
+    path "versions.yml"                                                                    , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    """
+    slow5tools f2s fast5_dir -d blow5_dir
+    slow5tools merge blow5_dir -o file.blow5
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        nanopolish: \$( slow5tools -V | head -n 1 | tail -c 6 )
+    END_VERSIONS
+    """
+}