Fix tests

nf-core · Jul 11, 2023 · a955751 · a955751
1 parent d5c67a7
commit a955751
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Showing 5 changed files with 71 additions and 35 deletions.
diff --git a/modules/nf-core/simpleaf/index/main.nf b/modules/nf-core/simpleaf/index/main.nf
@@ -1,5 +1,5 @@
 process SIMPLEAF_INDEX {
-    tag "$transcript_gtf"
+    tag "$genome_fasta $transcript_fasta"
     label 'process_high'
 
     conda "bioconda::simpleaf=0.14.1"
@@ -9,12 +9,12 @@ process SIMPLEAF_INDEX {
 
     input:
     path genome_fasta
+    path genome_gtf
     path transcript_fasta
-    path transcript_gtf
 
     output:
     path "salmon/index"              , emit: index
-    path "salmon/ref/t2g_3col.tsv" , emit: transcript_tsv
+    path "salmon/ref/t2g_3col.tsv"   , emit: transcript_tsv, optional: true
     path "salmon"                    , emit: salmon
     path "versions.yml"              , emit: versions
 
@@ -23,7 +23,7 @@ process SIMPLEAF_INDEX {
 
     script:
     def args = task.ext.args ?: ''
-    def seq_inputs = (params.transcript_fasta) ? "--refseq $transcript_fasta" : "--gtf $transcript_gtf"
+    def seq_inputs = (transcript_fasta) ? "--refseq $transcript_fasta" : "--gtf $genome_gtf --fasta $genome_fasta"
     """
     # export required var
     export ALEVIN_FRY_HOME=.
@@ -35,7 +35,6 @@ process SIMPLEAF_INDEX {
     simpleaf \\
         index \\
         --threads $task.cpus \\
-        --fasta $genome_fasta \\
         $seq_inputs \\
         $args \\
         -o salmon

diff --git a/modules/nf-core/simpleaf/quant/main.nf b/modules/nf-core/simpleaf/quant/main.nf
@@ -12,10 +12,10 @@ process SIMPLEAF_QUANT {
     // Input reads are expected to come as: [ meta, [ pair1_read1, pair1_read2, pair2_read1, pair2_read2 ] ]
     // Input array for a sample is created in the same order reads appear in samplesheet as pairs from replicates are appended to array.
     //
-    tuple val(meta), path(reads)
+    tuple val(meta), val(chemistry), path(reads)
     path index
+    val resolution
     path txp2gene
-    val chemistry
     path whitelist
 
     output:
@@ -30,20 +30,15 @@ process SIMPLEAF_QUANT {
     def args_list = args.tokenize()
     def prefix    = task.ext.prefix ?: "${meta.id}"
 
-    //
-    // check if users are using one of the mutually excludable parameters:
-    //    e.g -k,--knee | -e,--expect-cells | -f, --forced-cells
-    //
-    if (args_list.any { it in ['-k', '--knee', '-e', '--expect-cells', '-f', '--forced-cells']} || meta.expected_cells) {
-        unfiltered_command = ""
-        save_whitelist     = ""
-    } else {
-        unfiltered_command = "-u whitelist.uncompressed.txt"
-        save_whitelist     = "mv whitelist.uncompressed.txt ${prefix}_alevin_results/"
+    unfiltered_command = ""
+    if (whitelist) {
+        unfiltered_command = "-u <(gzip -dcf ${whitelist})"
     }
 
-    // expected cells
-    def expect_cells = meta.expected_cells ? "--expect-cells $meta.expected_cells" : ''
+    t2g_command = ""
+    if (txp2gene) {
+        t2g_command = "-m $txp2gene"
+    }
 
     // separate forward from reverse pairs
     def (forward, reverse) = reads.collate(2).transpose()
@@ -55,20 +50,18 @@ process SIMPLEAF_QUANT {
     simpleaf set-paths
 
     # run simpleaf quant
-    gzip -dcf $whitelist > whitelist.uncompressed.txt
     simpleaf quant \\
         -1 ${forward.join( "," )} \\
         -2 ${reverse.join( "," )} \\
         -i ${index} \\
+        -c $chemistry \\
+        -r $resolution \\
         -o ${prefix}_alevin_results \\
-        -m $txp2gene \\
         -t $task.cpus \\
-        -c $chemistry \\
-        $expect_cells \\
+        $t2g_command \\
         $unfiltered_command \\
         $args
 
-    $save_whitelist
     [[ ! -f ${prefix}_alevin_results/af_quant/all_freq.bin ]] && cp ${prefix}_alevin_results/af_quant/permit_freq.bin ${prefix}_alevin_results/af_quant/all_freq.bin
 
     cat <<-END_VERSIONS > versions.yml

diff --git a/tests/modules/nf-core/simpleaf/index/main.nf b/tests/modules/nf-core/simpleaf/index/main.nf
@@ -4,15 +4,25 @@ nextflow.enable.dsl = 2
 
 include { SIMPLEAF_INDEX } from '../../../../../modules/nf-core/simpleaf/index/main.nf'
 
-workflow test_simpleaf_index {
+workflow test_simpleaf_index_expanded {
 
     genome_fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    transcriptome_fasta = file(params.test_data['homo_sapiens']['genome']['transcriptome_fasta'], checkIfExists: true)
     gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
 
     SIMPLEAF_INDEX ( 
         genome_fasta,
+        gtf,
+        []
+    )
+}
+
+workflow test_simpleaf_index_direct {
+
+    transcriptome_fasta = file(params.test_data['homo_sapiens']['genome']['transcriptome_fasta'], checkIfExists: true)
+
+    SIMPLEAF_INDEX (
+        [],
+        [], 
         transcriptome_fasta,
-        gtf
     )
 }
diff --git a/tests/modules/nf-core/simpleaf/quant/main.nf b/tests/modules/nf-core/simpleaf/quant/main.nf
@@ -7,29 +7,57 @@ include { SIMPLEAF_QUANT } from '../../../../../modules/nf-core/simpleaf/quant/m
 
 workflow test_simpleaf_quant {
 
+    genome_fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
+
+    SIMPLEAF_INDEX (
+        genome_fasta,
+        gtf,
+        []
+    )
+
     input = [ 
         [ id:'test_10x', single_end:false, strandedness:'auto'  ], // meta map
+        '10xv3', // Chemistry
         [ 
             file(params.test_data['homo_sapiens']['10xgenomics']['cellranger']['test_10x_5k_cmvpos_tcells_gex1_fastq_1_gz'], checkIfExists: true),
             file(params.test_data['homo_sapiens']['10xgenomics']['cellranger']['test_10x_5k_cmvpos_tcells_gex1_fastq_2_gz'], checkIfExists: true)
         ]
     ]
 
-    genome_fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    SIMPLEAF_QUANT ( 
+        input,
+        SIMPLEAF_INDEX.out.index,
+        'cr-like',
+        SIMPLEAF_INDEX.out.transcript_tsv,
+        []
+    )
+}
+
+workflow test_simpleaf_quant_nogtf {
+
     transcriptome_fasta = file(params.test_data['homo_sapiens']['genome']['transcriptome_fasta'], checkIfExists: true)
-    gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
 
-    SIMPLEAF_INDEX ( 
-        genome_fasta,
+    SIMPLEAF_INDEX (
+        [],
+        [], 
         transcriptome_fasta,
-        gtf
     )
 
+    input = [ 
+        [ id:'test_10x', single_end:false, strandedness:'auto'  ], // meta map
+        '10xv3', // Chemistry
+        [ 
+            file(params.test_data['homo_sapiens']['10xgenomics']['cellranger']['test_10x_5k_cmvpos_tcells_gex1_fastq_1_gz'], checkIfExists: true),
+            file(params.test_data['homo_sapiens']['10xgenomics']['cellranger']['test_10x_5k_cmvpos_tcells_gex1_fastq_2_gz'], checkIfExists: true)
+        ]
+    ]
+
     SIMPLEAF_QUANT ( 
         input,
         SIMPLEAF_INDEX.out.index,
-        SIMPLEAF_INDEX.out.transcript_tsv,
-        '10xv3',
+        'cr-like',
+        [],
         []
     )
 }
diff --git a/tests/modules/nf-core/simpleaf/quant/nextflow.config b/tests/modules/nf-core/simpleaf/quant/nextflow.config
@@ -2,4 +2,10 @@ process {
 
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
 
-}
+    withName: 'test_simpleaf_quant:SIMPLEAF_QUANT' {
+        ext.args = { "--knee" }
+    }
+    withName: 'test_simpleaf_quant_nogtf:SIMPLEAF_QUANT' {
+        ext.args = { "--knee" }
+    }
+}