| spark_binary |
path to the spark-submit executable script |
spark-submit |
NO |
|
| NGS_workspace |
path to the folder where all necessary files should be stored: FASTQs, reference genome |
- |
YES |
|
| bio_pipe_fastq |
mask path to the FASTQ file used in the analysis |
- |
YES |
e.g. /data/work/samples/chr*.fastq |
| bio_pipe_spark_connection |
id of the Airflow connection; refers to the master parameter of the spark-submit script |
- |
YES |
|
| bio_pipe_prefix |
prefix of the output files names |
- |
YES |
|
| bio_pipe_jar |
absolute path to the JAR of BioPipeline package |
- |
YES |
the absolute path to the jar stored in: tools/target/scala-2.11/BioPipeline-assembly-0.2-SNAPSHOT.jar |
| bio_pipe_cannoli |
absolute path to the JAR of Cannoli package |
- |
YES |
the absolute path to the jar stored in: tools/lib/cannoli-assembly-spark2_2.11-0.11.0-SNAPSHOT.jar |
| bio_pipe_aligner |
name of the alignment tool |
bowtie2 |
NO |
possible values: bowtie2, bwa |
| bio_pipe_snps_file |
absolute file to the file with the SNP |
- |
YES |
should be in the VCF format |
| bio_pipe_reference |
|
- |
YES |
|
|
|
|
|
|
| bio_pipe_fastqc_threads |
the number of threads for Fastqc |
1 |
NO |
|
|
|
|
|
|
| bio_pipe_alignment_additional_args |
additional arguments related to the Cannoli package in the alignment stage |
- |
NO |
|
| bio_pipe_alignment_tool_args |
additional arguments related to the executed tool in the alignment stage |
- |
NO |
|
| bio_pipe_sequence_dict |
absolute path to the sequence dictionary |
- |
NO |
Sequence dictionary will be evaluated within the alignment stage, loading the reference genome. This may lengthen the time of alignment. |
| bio_pipe_alignment_image |
Docker image used in the alignment stage |
bowtie2: quay.io/biocontainers/bowtie2:2.4.2--py38h1c8e9b9_0 bwa: quay.io/biocontainers/bwa:0.7.17--hed695b0_7 |
NO |
|
| bio_pipe_alignment_spark_num_executors |
the number of executors used in the alignment stage; refers to the num_executors parameter of the spark-submit script |
1 |
NO |
|
| bio_pipe_alignment_spark_executor_memory |
the amount of memory allocated to executors used in the alignment stage; refers to the executor-memory parameter of the spark-submit script |
2G |
NO |
|
| bio_pipe_alignment_spark_driver_memory |
the amount of memory allocated to the driver used in the alignment stage; refers to the driver-memory parameter of the spark-submit script |
2G |
NO |
|
|
|
|
|
|
| bio_pipe_variantcalling_spark_num_executors |
the number of executors used in the variant calling stage; refers to the num_executors parameter of the spark-submit script |
1 |
NO |
|
| bio_pipe_variantcalling_spark_executor_memory |
the amount of memory allocated to executors used in the variant calling stage; refers to the executor-memory parameter of the spark-submit script |
2G |
NO |
|
| bio_pipe_variantcalling_spark_driver_memory |
the amount of memory allocated to the driver used in the variant calling stage; refers to the executor-memory parameter of the spark-submit script |
2G |
NO |
|
| bio_pipe_variantcalling_additional_args |
additional arguments related to the Cannoli package in the variant calling stage |
- |
NO |
|
| bio_pipe_variantcalling_tool_args |
additional arguments related to the executed tool in the variant calling stage |
- |
NO |
|
| bio_pipe_variantcalling_image |
Docker image used in the variant calling stage |
quay.io/biocontainers/freebayes:1.3.2--py37h7c46602_1 |
NO |
|
|
|
|
|
|
| bio_pipe_annotation_spark_num_executors |
the number of executors used in the annotation stage; refers to the num_executors parameter of the spark-submit script |
1 |
NO |
|
| bio_pipe_annotation_spark_executor_memory |
the amount of memory allocated to executors used in the annotation stage; refers to the executor-memory parameter of the spark-submit script |
2G |
NO |
|
| bio_pipe_annotation_spark_driver_memory |
the amount of memory allocated to the driver used in the annotation stage; refers to the executor-memory parameter of the spark-submit script |
2G |
NO |
|
| bio_pipe_vep_cache |
absolute path to the folder with the cache of the VEP tool |
- |
YES |
|
| bio_pipe_annotation_additional_args |
additional arguments related to the Cannoli package in the annotation stage |
- |
NO |
|
| bio_pipe_annotation_tool_args |
additional arguments related to the executed tool in the annotation stage |
- |
NO |
|
| bio_pipe_annotation_image |
Docker image used in the annotation stage |
quay.io/biocontainers/ensembl-vep:100.2--pl526hecda079_0 |
NO |
|