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Input source-based paramter validation (BAM entry) #162

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Input source-based paramter validation (BAM entry) #162

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70 changes: 49 additions & 21 deletions workflows/clipseq.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -9,10 +9,10 @@ def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params)
// Validate input parameters
WorkflowClipseq.initialise(params, log)

// Check manditory input parameters to see if the files exist if they have been specified
// Check mandatory input parameters to see if the files exist if they have been specified
check_param_list = [
input: params.input,
fasta: params.fasta,
// fasta: params.fasta,
ncrna_fasta: params.ncrna_fasta,
gtf: params.gtf
]
Expand All @@ -25,10 +25,11 @@ for (param in check_param_list) {
}
}

// Check non-manditory input parameters to see if the files exist if they have been specified

// Check non-mandatory input parameters to see if the files exist if they have been specified
def checkPathParamList = [
params.multiqc_config,
params.fasta_fai,
// params.fasta_fai,
params.ncrna_fasta_fai,
params.genome_index,
params.ncrna_genome_index,
Expand All @@ -49,14 +50,41 @@ def checkPathParamList = [
]
for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } }

// Check input source and validate parameters
def checkInputParamList = []
println("source: ${params.source}")
if ((params.source ?: "fastq") == "fastq") {
checkInputParamList = [
params.fasta
// Add more as appropriate, remember to remove them from lists above, if required
]
println("fasta: ${params.fasta}")
} else if (params.source == "bam") {
checkInputParamList = [
params.genome_bam // Placeholder
]
} else {
exit 1, "Invalid source option: ${params.source}. Valid options: fastq, bam"
}

for (param in checkInputParamList) {
if (!param) {
exit 1, "Required parameter not specified: ${param} (input source: ${params.source})"
}
else {
file(param, checkIfExists: true)
}
}


// Define peak callers and check in list
caller_list = [ 'icount', 'paraclu', 'pureclip', 'clippy']
callers = params.peakcaller ? params.peakcaller.split(',').collect{ it.trim().toLowerCase() } : []
if ((caller_list + callers).unique().size() != caller_list.size()) {
exit 1, "Invalid variant caller option: ${params.peakcaller}. Valid options: ${caller_list.join(', ')}"
}

// // Stage dummy files to be used as an optional input where required
// Stage dummy files to be used as an optional input where required
ch_dummy_file = file("$projectDir/assets/dummy_file.txt", checkIfExists: true)
ch_dummy_file2 = file("$projectDir/assets/dummy_file2.txt", checkIfExists: true)

Expand Down Expand Up @@ -345,13 +373,13 @@ workflow CLIPSEQ {
ch_versions = ch_versions.mix(TRANSCRIPTOME_PROCESSING.out.versions)
ch_transcript_bam = TRANSCRIPTOME_PROCESSING.out.transcript_dedupe_bam
ch_transcript_bai = TRANSCRIPTOME_PROCESSING.out.transcript_dedupe_bai
ch_trans_crosslink_bed = TRANSCRIPTOME_PROCESSING.out.crosslink_bed
ch_trans_crosslink_bed = TRANSCRIPTOME_PROCESSING.out.crosslink_bed
ch_clippy_transcriptome_peaks = TRANSCRIPTOME_PROCESSING.out.clippy_peaks
ch_paraclu_transcriptome_peaks = TRANSCRIPTOME_PROCESSING.out.paraclu_peaks
}

//ch_genome_umi_log = Channel.empty()

// DEDUPLICATION //
if(params.source == "fastq" & params.run_dedup) {
// PREPARE CHANNELS
Expand Down Expand Up @@ -518,7 +546,7 @@ workflow CLIPSEQ {
ch_filtered_gtf.collect{ it[1] },
ch_fasta_fai.collect{ it[1] }
)

CLIPPY_CONSENSUS_PEAK_TABLE (
ch_all_crosslinks,
CLIPPY_GENOME_CONSENSUS.out.peaks,
Expand Down Expand Up @@ -547,7 +575,7 @@ workflow CLIPSEQ {
ICOUNTMINI_SIGXLS (
ch_genome_crosslink_group_resolved_bed,
ch_seg_resolved_gtf.collect{ it[1]}

)

ch_versions = ch_versions.mix(ICOUNTMINI_SIGXLS.out.versions)
Expand Down Expand Up @@ -625,7 +653,7 @@ workflow CLIPSEQ {

}



if('paraclu' in callers) {

Expand Down Expand Up @@ -671,9 +699,9 @@ workflow CLIPSEQ {

// Print initial channel contents for debugging
// ch_genome_peakcalling.view { item -> "Initial ch_genome_peakcalling item: $item" }

ch_genome_peakcalling
.branch { meta, bam, bai ->
.branch { meta, bam, bai ->
control: meta.control
no_control: !meta.control
}
Expand All @@ -685,9 +713,9 @@ workflow CLIPSEQ {

result.control
.map{ meta, bam, bai -> [meta.control, bam, bai, meta]
}.set{ ch_genome_peakcalling_withControlid }
}.set{ ch_genome_peakcalling_withControlid }

ch_temp_pureclip_input = ch_genome_peakcalling_withControlid.join(ch_genome_peakcalling_withid, by: 0)
ch_temp_pureclip_input = ch_genome_peakcalling_withControlid.join(ch_genome_peakcalling_withid, by: 0)
// Structure is now [ControlID, IPBam, IPBai, IPMeta, Controlbam, Controlbai]

// Check structure is what we expect
Expand All @@ -702,7 +730,7 @@ workflow CLIPSEQ {
ch_temp_pureclip_input
.map{ ControlID, IPBam, IPBai, IPMeta, Controlbam, Controlbai -> [IPMeta, IPBam, Controlbam ]}
.set{ ch_pureclip_bams_withcontrol }

ch_temp_pureclip_input
.map{ ControlID, IPBam, IPBai, IPMeta, Controlbam, Controlbai -> [IPMeta, IPBai, Controlbai ]}
.set{ ch_pureclip_bais_withcontrol }
Expand All @@ -713,12 +741,12 @@ workflow CLIPSEQ {
ch_fasta,
true
)

// Run PURECLIP for samples without control
result.no_control
.map{ meta, bam, bai -> [meta, bam, [] ]}
.set{ ch_pureclip_bams_nocontrol }

result.no_control
.map{ meta, bam, bai -> [meta, bai, [] ]}
.set{ ch_pureclip_bais_nocontrol }
Expand All @@ -741,15 +769,15 @@ workflow CLIPSEQ {
// After all the mixing
ch_pureclip_genome_peaks.join(ch_genome_crosslink_group_resolved_bed, by: 0)
.set{ temp_matched_channel }

temp_matched_channel
.map{ meta, peaks, crosslinks -> [meta, peaks] }
.set{ ch_pureclip_genome_peaks_matched }

temp_matched_channel
.map{ meta, peaks, crosslinks -> [meta, crosslinks] }
.set{ ch_genome_crosslink_bed_matched }

PEKA_PURECLIP(
ch_pureclip_genome_peaks_matched,
ch_genome_crosslink_bed_matched,
Expand Down Expand Up @@ -797,7 +825,7 @@ workflow CLIPSEQ {
ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml'))
ch_multiqc_files = ch_multiqc_files.mix(DUMP_SOFTWARE_VERSIONS.out.mqc_yml.collect())
ch_multiqc_files = ch_multiqc_files.mix(DUMP_SOFTWARE_VERSIONS.out.mqc_unique_yml.collect())

ch_multiqc_files = ch_multiqc_files.mix(FASTQ_FASTQC_UMITOOLS_TRIMGALORE.out.fastqc_zip.collect{it[1]}.ifEmpty([]))
ch_multiqc_files = ch_multiqc_files.mix(FASTQ_FASTQC_UMITOOLS_TRIMGALORE.out.trim_zip.collect{it[1]}.ifEmpty([]))
ch_multiqc_files = ch_multiqc_files.mix(FASTQ_FASTQC_UMITOOLS_TRIMGALORE.out.trim_log.collect{it[1]}.ifEmpty([]))
Expand Down
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