Hi-C workflow #139
Hi-C workflow #139
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Snyk Container found more than 20 potential problems in the proposed changes. Check the Files changed tab for more details.
Co-authored-by: Andrew Frantz <[email protected]>
| "make_hic_reference.restriction_sites": ["^GATC", "^GATC", "A^GATCT", "A^AGCTT", "G^ANTC", "AT^CGAT"], | ||
| "make_hic_reference.restriction_sites_names": ["mboi", "dpnii", "bglii", "hindiii", "hinfi", "clai"] |
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Should these be moved to the defaults of the workflow? In what situations would a user want to use something different?
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Restriction sites are custom to the experiment. I put several of the most common ones here, but there's no reason someone couldn't be using a different cut site.
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| FROM ghcr.io/stjudecloud/bedtools:branch-hic_workflow-2.31.1-0 AS bedtools | |||
Check notice
Code scanning / Snyk Container
Low severity - CVE-2024-13176 vulnerability in openssl Note
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| FROM ubuntu:22.04 AS builder | |||
Check notice
Code scanning / Snyk Container
Low severity - CVE-2024-13176 vulnerability in openssl Note
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| FROM aidenlab/juicer:v2.0.1 AS builder | |||
Check failure
Code scanning / Snyk Container
Critical severity - Integer Overflow or Wraparound vulnerability in expat Critical
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| FROM aidenlab/juicer:v2.0.1 AS builder | |||
Check failure
Code scanning / Snyk Container
Critical severity - Integer Overflow or Wraparound vulnerability in expat Critical
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| FROM aidenlab/juicer:v2.0.1 AS builder | |||
Check failure
Code scanning / Snyk Container
High severity - XML External Entity (XXE) Injection vulnerability in expat High
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| FROM aidenlab/juicer:v2.0.1 AS builder | |||
Check notice
Code scanning / Snyk Container
Low severity - CVE-2024-50602 vulnerability in expat Note
| @@ -0,0 +1,15 @@ | |||
| FROM aidenlab/juicer:v2.0.1 AS builder | |||
Check warning
Code scanning / Snyk Container
Medium severity - Algorithmic Complexity vulnerability in libtasn1 Medium
| @@ -0,0 +1,15 @@ | |||
| FROM aidenlab/juicer:v2.0.1 AS builder | |||
Check notice
Code scanning / Snyk Container
Low severity - CVE-2024-6119 vulnerability in openssl Note
| @@ -0,0 +1,15 @@ | |||
| FROM aidenlab/juicer:v2.0.1 AS builder | |||
Check notice
Code scanning / Snyk Container
Low severity - CVE-2024-9143 vulnerability in openssl Note
| @@ -0,0 +1,15 @@ | |||
| FROM aidenlab/juicer:v2.0.1 AS builder | |||
Check notice
Code scanning / Snyk Container
Low severity - CVE-2024-13176 vulnerability in openssl Note
Implements a workflow to generate a bowtie2-aligned BAM and a
.hicfile for analysis. This utilizes the commonly used HiC-Pro workflow.