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Add working basic test to begin

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This commit is contained in:
James Fellows Yates 2022-03-21 20:28:09 +01:00
parent cd9e3c604c
commit 81bfb629ca
5 changed files with 35 additions and 9 deletions
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1
.github/workflows/ci.yml vendored
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@ -48,3 +48,4 @@ jobs:
# Remember that you can parallelise this by using strategy.matrix # Remember that you can parallelise this by using strategy.matrix
run: | run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
# TODO Add test that runs with pre-downloaded and decompressed databases

16
conf/modules.config
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@ -26,6 +26,22 @@ process {
] ]
} }
withName: DATABASE_CHECK {
publishDir = [
path: { "${params.outdir}/pipeline_info" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
withName: UNTAR {
publishDir = [
path: { "${params.outdir}/databases" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
withName: FASTQC { withName: FASTQC {
ext.args = '--quiet' ext.args = '--quiet'
ext.prefix = { "${meta.id}_${meta.run_accession}_raw" } ext.prefix = { "${meta.id}_${meta.run_accession}_raw" }

8
conf/test.config
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@ -22,6 +22,12 @@ params {
// Input data // Input data
// TODO nf-core: Specify the paths to your test data on nf-core/test-datasets // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
// TODO nf-core: Give any required params for the test so that command line flags are not needed // TODO nf-core: Give any required params for the test so that command line flags are not needed
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/samplesheet.csv' input = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/samplesheet.csv'
outdir = "./results"
// TODO replace with official once ready
databases = 'https://raw.githubusercontent.com/jfy133/nf-core-test-datasets/taxprofiler/database.csv'
run_kraken2 = true
run_malt = true
shortread_clipmerge = true
} }

6
subworkflows/local/input_check.nf
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@ -30,7 +30,7 @@ workflow INPUT_CHECK {
.set { nanopore } .set { nanopore }
parsed_samplesheet.fasta parsed_samplesheet.fasta
.map { create_fasta_channels(it) } .map { create_fasta_channel(it) }
.dump(tag: "fasta_channel_init") .dump(tag: "fasta_channel_init")
.set { fasta } .set { fasta }
@ -42,7 +42,7 @@ workflow INPUT_CHECK {
} }
// Function to get list of [ meta, [ fastq_1, fastq_2 ] ] // Function to get list of [ meta, [ fastq_1, fastq_2 ] ]
def create_fastq_channels(LinkedHashMap row) { def create_fastq_channel(LinkedHashMap row) {
// create meta map // create meta map
def meta = [:] def meta = [:]
meta.id = row.sample meta.id = row.sample
@ -74,7 +74,7 @@ def create_fastq_channels(LinkedHashMap row) {
} }
// Function to get list of [ meta, fasta ] // Function to get list of [ meta, fasta ]
def create_fasta_channels(LinkedHashMap row) { def create_fasta_channel(LinkedHashMap row) {
def meta = [:] def meta = [:]
meta.id = row.sample meta.id = row.sample
meta.run_accession = row.run_accession meta.run_accession = row.run_accession

13
workflows/taxprofiler.nf
View file

@ -101,7 +101,9 @@ workflow TAXPROFILER {
// PERFORM PREPROCESSING // PERFORM PREPROCESSING
// //
if ( params.shortread_clipmerge ) { if ( params.shortread_clipmerge ) {
SHORTREAD_PREPROCESSING ( INPUT_CHECK.out.fastq ) ch_shortreads_preprocessed = SHORTREAD_PREPROCESSING ( INPUT_CHECK.out.fastq ).reads
} else {
ch_shortreads_preprocessed = INPUT_CHECK.out.fastq
} }
if ( params.longread_clip ) { if ( params.longread_clip ) {
@ -113,9 +115,10 @@ workflow TAXPROFILER {
} }
// //
// PERFORM RUN MERGING // PERFORM SHORT READ RUN MERGING
// TODO: Check not necessary for long reads too?
// //
ch_processed_for_combine = SHORTREAD_PREPROCESSING.out.reads ch_processed_for_combine = ch_shortreads_preprocessed
.dump(tag: "prep_for_combine_grouping") .dump(tag: "prep_for_combine_grouping")
.map { .map {
meta, reads -> meta, reads ->
@ -140,7 +143,7 @@ workflow TAXPROFILER {
// COMBINE READS WITH POSSIBLE DATABASES // COMBINE READS WITH POSSIBLE DATABASES
// //
// output [DUMP: reads_plus_db] [['id':'2612', 'run_accession':'combined', 'instrument_platform':'ILLUMINA', 'single_end':1], <reads_path>/2612.merged.fastq.gz, ['tool':'malt', 'db_name':'mal95', 'db_params':'"-id 90"'], <db_path>/malt90] // e.g. output [DUMP: reads_plus_db] [['id':'2612', 'run_accession':'combined', 'instrument_platform':'ILLUMINA', 'single_end':1], <reads_path>/2612.merged.fastq.gz, ['tool':'malt', 'db_name':'mal95', 'db_params':'"-id 90"'], <db_path>/malt90]
ch_input_for_profiling = ch_reads_for_profiling ch_input_for_profiling = ch_reads_for_profiling
.mix( ch_longreads_preprocessed ) .mix( ch_longreads_preprocessed )
.combine(DB_CHECK.out.dbs) .combine(DB_CHECK.out.dbs)
@ -152,7 +155,7 @@ workflow TAXPROFILER {
} }
// //
// PREP PROFILER INPUT CHANNELS ON PER TOOL BASIS // PREPARE PROFILER INPUT CHANNELS
// //
// We groupTuple to have all samples in one channel for MALT as database // We groupTuple to have all samples in one channel for MALT as database