Fix add library complexity (#159)

* Add Singularity bind for presets ending with "s" * Set APPTAINER_BIND environment variable in cli_pipeline function * Update Singularity and Slurm configurations * Refactor APPTAINER_BINDPATH in cli_pipeline function * Increase runtime for trimgalore_paired rule * Refactor is_paired method in AssayNonIP class * Add rule align_single_spikein for aligning single spikein samples * add align single to ruleorder * Increase number of jobs to 100 in slurm-singularity profile * Refactor align_single_spikein rule * fix exo align mem resources * Increase runtime for deeptools_make_bigwigs rules * Add retries option to config.yaml * Add fastq_screen flag to Output class * Update QCFiles instantiation in NonRNAOutput and ChIPOutput * Add library complexity flag to QCFiles instantiation * add lib comp to config and test * fix typo in config yaml * fix align paired rule * increase memory on sort bam spikein --------- Co-authored-by: alsmith <[email protected]>
alsmith151 · Mar 26, 2024 · 23d5210 · 23d5210
1 parent fdd002d
commit 23d5210
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Showing 4 changed files with 9 additions and 3 deletions.
diff --git a/seqnado/config.py b/seqnado/config.py
@@ -86,7 +86,11 @@ def setup_configuration(assay, genome, template_data):
             "Path to fastqscreen config:",
             default="/ceph/project/milne_group/shared/seqnado_reference/fastqscreen_reference/fastq_screen.conf",
         )
-
+
+    # Library Complexity
+    template_data["library_complexity"] = get_user_input(
+        "Calculate library complexity? (yes/no)", default="no", is_boolean=True
+    )
     # Blacklist
     template_data["remove_blacklist"] = get_user_input(
         "Do you want to remove blacklist regions? (yes/no)",

diff --git a/seqnado/workflow/config/config.yaml.jinja b/seqnado/workflow/config/config.yaml.jinja
@@ -16,7 +16,7 @@ genome:
 
 fastq_screen: "{{fastq_screen}}"
 fastq_screen_config: "{{fastq_screen_config}}"
-
+library_complexity: "{{library_complexity}}"
 remove_blacklist: "{{remove_blacklist}}"
 blacklist: "{{blacklist}}"
 

diff --git a/seqnado/workflow/rules/exogenous_norm.smk b/seqnado/workflow/rules/exogenous_norm.smk
@@ -23,10 +23,11 @@ use rule sort_bam as sort_bam_spikein with:
         bam="seqnado_output/aligned/spikein/raw/{sample}.bam",
     output:
         bam=temp("seqnado_output/aligned/spikein/sorted/{sample}.bam"),
+    resources:
+        mem=lambda wildcards, attempt: f"{8 * 2 ** (attempt - 1)}GB",
     log:
         "seqnado_output/logs/aligned_spikein/{sample}_sort.log",
 
-
 use rule index_bam as index_bam_spikein with:
     input:
         bam=rules.sort_bam_spikein.output.bam,

diff --git a/tests/test_pipelines.py b/tests/test_pipelines.py
@@ -200,6 +200,7 @@ def user_inputs(test_data_path, indicies, chromsizes, assay, assay_type, gtf, bl
         "gtf": str(gtf),
         "blacklist": str(blacklist),
         "fastq_screen": "no",
+        "library_complexity": "yes",
         "remove_blacklist": "yes",
     }