Sergey Mitrofanov

Pack (gzip) output good and bad reads

4

I think it would be great to pack the output reads (good & bad)!

default good folder

3

Hello! Due to `default = "good"` in [line 27](https://github.com/OpenGene/AfterQC/blob/master/after.py#L28), the description in line 28 contains a mistake. If option `-g` is not set by user, then the `good` folder will...

What do you think about some kind of parallel mode for processing a single pair of PE reads (`-1` and `-2` options) when `good` reads are to be generated?

An input with two possible types: string and File with secondaryFiles

1

Hello! How should I specify the input that can be on of two types: `string` or `File`. When `File`, a `secondaryFiles` parameter is needed. More over, the same `inputBinding` section...

python3 support

3

Hello! Does your tool support python3?

ERROR preprocess: vcf.c:3472: bcf_update_format: Assertion `!fmt->p_free' failed.

7

I can't get rid of this: ``` root@86876e01e030:/outputs# /opt/hap.py/bin/hap.py --threads $(nproc) --gender auto --reference /outputs/ref/human_g1k_v37/human_g1k_v37.fasta --false-positives /outputs/precFDA/challenge4-fullset.bed --report-prefix /outputs/test012_07_NovoalignGATKHC_1_src /outputs/precFDA/challenge4-fullset.vcf.gz /outputs/precFDA/challenge_results/NovoalignGATKHC_1.vcf.gz 2019-09-10 15:26:22,969 WARNING No reference file found at default...

Option --no-rebuild-external doesn't exist

1

Hello! The option `--no-rebuild-external` doesn't exist in the `install.py` script but is mentioned in the `README.md`.

I suggest: ``` export PATH="/opt/hap.py/bin:$PATH" ```

Hello! This step doesn't work now: https://github.com/Illumina/hap.py/blob/dac84d9c5aa50ee805de2edb7af10e6e1a58721a/Dockerfile#L22 I suggest: ``` RUN add-apt-repository -y ppa:openjdk-r/ppa \ && apt-get update \ && apt-get --yes --no-install-recommends install \ openjdk-8-jdk ```

Is it possible to run EH in parallel for a big catalog?

2

Hello! Egor, is it possible to run EH in parallel? I have many STR's in my catalog and a lot of samples, so it would be great to process them...