chore: add temp flags (#428)

IKIM-Essen · Dec 22, 2021 · a0e3d96 · a0e3d96
1 parent 300decd
commit a0e3d96
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Showing 9 changed files with 36 additions and 34 deletions.
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -76,12 +76,12 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      # - name: Cache conda dependencies
-      #   uses: actions/cache@v2
-      #   with:
-      #     path: |
-      #       .tests/.snakemake/conda
-      #     key: technology-${{ runner.os }}-${{ matrix.rule }}-${{ matrix.technology }}-${{ matrix.seq_method }}-${{ hashFiles('*.tests/.snakemake/conda/*.yaml') }}
+      # android - will release about 10 GB if you don't need Android
+      # dotnet  - will release about 20 GB if you don't need .NET
+      - name: Free up some disk sapce
+        run: |
+          sudo rm -rf /usr/local/lib/android
+          sudo rm -rf /usr/share/dotnet
 
       - name: Prepare test data for all technologies
         if: steps.test-data.outputs.cache-hit != true && (startsWith(matrix.rule, 'all') && matrix.technology == 'all' || matrix.rule == 'compare_assemblers')

diff --git a/workflow/rules/assembly.smk b/workflow/rules/assembly.smk
@@ -93,7 +93,7 @@ rule spades_assemble_se:
     input:
         get_reads_after_qc,
     output:
-        "results/{date}/assembly/{sample}/spades-se/{sample}.contigs.fasta",
+        temp("results/{date}/assembly/{sample}/spades-se/{sample}.contigs.fasta"),
     log:
         "logs/{date}/spades/se/{sample}.log",
     conda:
@@ -112,7 +112,7 @@ rule check_contigs:
     input:
         get_contigs,
     output:
-        "results/{date}/contigs/checked/{sample}.fasta",
+        temp("results/{date}/contigs/checked/{sample}.fasta"),
     log:
         "logs/{date}/check_contigs/{sample}.log",
     conda:
@@ -146,7 +146,7 @@ rule filter_chr0:
     input:
         "results/{date}/contigs/ordered-unfiltered/{sample}.fasta",
     output:
-        "results/{date}/contigs/ordered/{sample}.fasta",
+        temp("results/{date}/contigs/ordered/{sample}.fasta"),
     log:
         "logs/{date}/ragoo/{sample}_cleaned.log",
     conda:
@@ -206,7 +206,7 @@ rule aggregate_polished_de_novo_sequences:
     input:
         get_polished_sequence,
     output:
-        "results/{date}/contigs/polished/{sample}.fasta",
+        temp("results/{date}/contigs/polished/{sample}.fasta"),
     log:
         "logs/{date}/aggregate_polished_de_novo_sequences/{sample}.log",
     conda:
@@ -219,7 +219,7 @@ rule aggregate_fallback_sequences:
     input:
         get_fallback_sequence,
     output:
-        "results/{date}/contigs/fallback/{sample}.fasta",
+        temp("results/{date}/contigs/fallback/{sample}.fasta"),
     log:
         "logs/{date}/aggregate_fallback_sequences/{sample}.log",
     conda:
@@ -233,7 +233,7 @@ rule align_contigs:
         target="resources/genomes/main.fasta",
         query=get_quast_fastas,
     output:
-        "results/{date}/aligned/ref~main/{stage}~{sample}.bam",
+        temp("results/{date}/aligned/ref~main/{stage}~{sample}.bam"),
     log:
         "results/{date}/aligned/ref~main/{stage}~{sample}.log",
     conda:

diff --git a/workflow/rules/long_read.smk b/workflow/rules/long_read.smk
@@ -8,7 +8,7 @@ rule nanoQC:
     input:
         get_reads_by_stage,
     output:
-        "results/{date}/qc/nanoQC/{sample}/{stage}/nanoQC.html",
+        temp("results/{date}/qc/nanoQC/{sample}/{stage}/nanoQC.html"),
     log:
         "logs/{date}/nanoQC/{sample}_{stage}.log",
     params:
@@ -23,7 +23,7 @@ rule count_fastq_reads:
     input:
         get_reads_by_stage,
     output:
-        "results/{date}/tables/fastq-read-counts/{stage}~{sample}.txt",
+        temp("results/{date}/tables/fastq-read-counts/{stage}~{sample}.txt"),
     log:
         "logs/{date}/count_reads/{stage}~{sample}.log",
     conda:
@@ -36,7 +36,7 @@ rule porechop_adapter_barcode_trimming:
     input:
         get_fastqs,
     output:
-        "results/{date}/trimmed/porechop/adapter_barcode_trimming/{sample}.fastq",
+        temp("results/{date}/trimmed/porechop/adapter_barcode_trimming/{sample}.fastq"),
     conda:
         "../envs/porechop.yaml"
     log:
@@ -68,7 +68,7 @@ rule porechop_primer_trimming:
         ),
         repl_flag="results/.indicators/replacement_notice.txt",
     output:
-        "results/{date}/trimmed/porechop/primer_clipped/{sample}.fastq",
+        temp("results/{date}/trimmed/porechop/primer_clipped/{sample}.fastq"),
     conda:
         "../envs/primechop.yaml"
     log:
@@ -82,7 +82,7 @@ rule nanofilt:
     input:
         "results/{date}/trimmed/porechop/primer_clipped/{sample}.fastq",
     output:
-        "results/{date}/trimmed/nanofilt/{sample}.fastq",
+        temp("results/{date}/trimmed/nanofilt/{sample}.fastq"),
     log:
         "logs/{date}/nanofilt/{sample}.log",
     params:
@@ -126,7 +126,7 @@ use rule assembly_polishing_ont as medaka_consensus_reference with:
         fasta="results/{date}/corrected/{sample}/{sample}.correctedReads.fasta.gz",
         reference="resources/genomes/main.fasta",
     output:
-        "results/{date}/consensus/medaka/{sample}/{sample}.fasta",
+        temp("results/{date}/consensus/medaka/{sample}/{sample}.fasta"),
 
 
 # polish consensus
@@ -136,7 +136,7 @@ rule bcftools_consensus_ont:
         bcf="results/{date}/filtered-calls/ref~{sample}/{sample}.subclonal.high+moderate-impact.bcf",  # clonal vs. subclonal?
         bcfidx="results/{date}/filtered-calls/ref~{sample}/{sample}.subclonal.high+moderate-impact.bcf.csi",
     output:
-        "results/{date}/consensus/bcftools/{sample}.fasta",
+        temp("results/{date}/consensus/bcftools/{sample}.fasta"),
     log:
         "logs/{date}/bcftools-consensus-ont/{sample}.log",
     conda:

diff --git a/workflow/rules/pseudoassembly.smk b/workflow/rules/pseudoassembly.smk
@@ -35,7 +35,7 @@ rule compare_assemblies:
         assembly="results/{date}/contigs/polished/{sample}.fasta",
         pseudoassembly="results/{date}/contigs/pseudoassembled/{sample}.fasta",
     output:
-        "results/{date}/aligned/assemblies/{sample}.bam",
+        temp("results/{date}/aligned/assemblies/{sample}.bam"),
     log:
         "logs/{date}/aligned/assemblies/{sample}log",
     conda:

diff --git a/workflow/rules/read_clipping.smk b/workflow/rules/read_clipping.smk
@@ -8,7 +8,7 @@ rule samtools_sort:
     input:
         get_samtools_sort_input,
     output:
-        "results/{date}/read-sorted/{read_type}~{sorted_by}/{sample}.{stage}.bam",
+        temp("results/{date}/read-sorted/{read_type}~{sorted_by}/{sample}.{stage}.bam"),
     params:
         extra=(
             lambda wildcards: "-n -m 4G" if wildcards.sorted_by == "name" else "-m 4G"
@@ -56,7 +56,9 @@ rule fgbio:
             reference=config["adapters"]["amplicon-reference"]
         ),
     output:
-        "results/{date}/read-clipping/hardclipped/{read_type}/{sample}/{sample}.bam",
+        temp(
+            "results/{date}/read-clipping/hardclipped/{read_type}/{sample}/{sample}.bam"
+        ),
     log:
         "logs/{date}/fgbio/{read_type}/{sample}.log",
     conda:
@@ -69,8 +71,8 @@ rule samtools_fastq_pe:
     input:
         bam="results/{date}/read-sorted/pe~name/{sample}.hardclipped.bam",
     output:
-        fq1="results/{date}/read-clipping/fastq/pe/{sample}.1.fastq.gz",
-        fq2="results/{date}/read-clipping/fastq/pe/{sample}.2.fastq.gz",
+        fq1=temp("results/{date}/read-clipping/fastq/pe/{sample}.1.fastq.gz"),
+        fq2=temp("results/{date}/read-clipping/fastq/pe/{sample}.2.fastq.gz"),
     log:
         "logs/{date}/samtools_fastq/pe/{sample}.log",
     conda:
@@ -84,7 +86,7 @@ rule samtools_fastq_se:
     input:
         bam="results/{date}/read-sorted/se~name/{sample}.hardclipped.bam",
     output:
-        "results/{date}/read-clipping/fastq/se/{sample}.fastq",
+        temp("results/{date}/read-clipping/fastq/se/{sample}.fastq"),
     log:
         "logs/{date}/samtools_fastq/se/{sample}.log",
     conda:

diff --git a/workflow/rules/read_mapping.smk b/workflow/rules/read_mapping.smk
@@ -81,7 +81,7 @@ rule samtools_calmd:
         aln=get_recal_input,
         ref=get_reference(),
     output:
-        "results/{date}/recal/ref~{reference}/{sample}.bam",
+        temp("results/{date}/recal/ref~{reference}/{sample}.bam"),
     log:
         "logs/{date}/samtools-calmd/ref~{reference}/{sample}.log",
     params:

diff --git a/workflow/rules/read_trimming.smk b/workflow/rules/read_trimming.smk
@@ -35,9 +35,9 @@ rule fastp_se:
     input:
         sample=get_fastqs,
     output:
-        trimmed="results/{date}/trimmed/fastp-se/{sample}.fastq.gz",
-        html="results/{date}/trimmed/fastp-se/{sample}.html",
-        json="results/{date}/trimmed/fastp-se/{sample}.fastp.json",
+        trimmed=temp("results/{date}/trimmed/fastp-se/{sample}.fastq.gz"),
+        html=temp("results/{date}/trimmed/fastp-se/{sample}.html"),
+        json=temp("results/{date}/trimmed/fastp-se/{sample}.fastp.json"),
     params:
         adapters=get_adapters,
         extra="--qualified_quality_phred {} ".format(

diff --git a/workflow/rules/strain_calling.smk b/workflow/rules/strain_calling.smk
@@ -50,8 +50,8 @@ rule kallisto_metrics:
     input:
         get_reads_after_qc,
     output:
-        avg_read_length="results/{date}/tables/avg_read_length/{sample}.txt",
-        standard_deviation="results/{date}/tables/standard_deviation/{sample}.txt",
+        avg_read_length=temp("results/{date}/tables/avg_read_length/{sample}.txt"),
+        standard_deviation=temp("results/{date}/tables/standard_deviation/{sample}.txt"),
     log:
         "logs/{date}/kallisto/metrics/{sample}.log",
     conda:

diff --git a/workflow/rules/variant_calling.smk b/workflow/rules/variant_calling.smk
@@ -94,7 +94,7 @@ rule vcf_2_bcf:
     input:
         "results/{date}/candidate-calls/ref~{reference}/{sample}.{varrange}.vcf",
     output:
-        "results/{date}/candidate-calls/ref~{reference}/{sample}.{varrange}.bcf",
+        temp("results/{date}/candidate-calls/ref~{reference}/{sample}.{varrange}.bcf"),
     log:
         "logs/{date}/vcf_2_bcf/ref~{reference}/{sample}.{varrange}.log",
     conda:
@@ -122,7 +122,7 @@ rule varlociraptor_alignment_properties:
         ref_idx=get_reference(".fai"),
         bam="results/{date}/recal/ref~{reference}/{sample}.bam",
     output:
-        "results/{date}/alignment-properties/ref~{reference}/{sample}.json",
+        temp("results/{date}/alignment-properties/ref~{reference}/{sample}.json"),
     log:
         "logs/{date}/varlociraptor/estimate-alignment-properties/ref~{reference}/{sample}.log",
     conda:
@@ -141,7 +141,7 @@ rule varlociraptor_preprocess:
         bam="results/{date}/recal/ref~{reference}/{sample}.bam",
         bai="results/{date}/recal/ref~{reference}/{sample}.bam.bai",
     output:
-        "results/{date}/observations/ref~{reference}/{sample}.{varrange}.bcf",
+        temp("results/{date}/observations/ref~{reference}/{sample}.{varrange}.bcf"),
     params:
         depth=config["variant-calling"]["max-read-depth"],
     log: