Repository Analysis

bioconda/bioconda-recipes

Conda recipes for the bioconda channel.

3.9 Likely human-written View on GitHub

Analysis Overview

This report presents the forensic synthetic code analysis of bioconda/bioconda-recipes, a Shell project with 1,857 GitHub stars. SynthScan v2.0 examined 887,361 lines of code across 22911 source files, recording 1377 pattern matches distributed across 13 syntactic categories. The overall adjusted score of 3.9 places this repository in the Likely human-written band.

The scanner applied 160+ deterministic lexical heuristics, multi-line block detectors, abstract syntax tree depth profilers, and a cross-file Jaccard similarity matrix to construct a statistically normalised synthetic code estimate. All matches are individually weighted by severity coefficient and contextual multiplier before summation, and the resulting headline score is temporally discounted to account for the repository's development history relative to the commercial emergence of large language model coding tooling (November 2022 onward).

3.9
Adjusted Score
3.9
Raw Score
100%
Time Factor
2026-08-09
Last Push
1.9K
Stars
Shell
Language
887.4K
Lines of Code
22.9K
Files
1.4K
Pattern Hits
2026-08-09
Scan Date
0.02
HC Hit Rate

What These Metrics Mean

Adjusted Score
Primary synthetic code indicator. Raw score normalised per 1,000 lines of code and multiplied by the temporal discount factor. This is the definitive comparative metric — use it to rank repositories by AI authorship density.
Raw Score
The unmodified sum of all severity-weighted, context-multiplied pattern match scores before temporal discounting. Reflects the absolute signal strength independent of when the repository was last active.
Time Factor
The temporal discount multiplier (0–100%) applied to the raw score. Repositories last updated before ChatGPT's launch (Nov 2022) receive a 5% factor. Full signal is only assigned to repositories active in the post-adoption era (Jan 2024+).
Pattern Hits
Total count of individual pattern matches across all files and categories. A high hit count with a low score may indicate a very large codebase with isolated AI snippets; a low count with a high score indicates dense, concentrated AI signatures.
HC Hit Rate
High+Critical pattern hits per file, averaged across the repository. This orthogonal signal catches repositories where a few files are densely packed with high-severity AI tells — a strong indicator even when the normalised score appears moderate due to codebase size.
Lines of Code / Files
Total lines and files analysed. The scanner examines 94 file extensions. These denominators are used to normalise the score, enabling fair comparison between repositories of vastly different sizes.

Score History

Longitudinal tracking requires multiple scan runs. Once this repository is re-scanned after new commits land, this chart will visualise how the synthetic code signal evolves over time — enabling you to detect whether AI authorship is growing, stabilising, or being actively corrected by human engineers.

No multi-scan history yet — run the scanner again to build trend data.

Severity Breakdown

Classifies detected patterns by their diagnostic confidence and structural impact. CRITICAL patterns (coefficient 10) represent definitive synthetic signatures — hallucinated imports, explicit LLM attribution metadata — virtually never produced by human authors. HIGH (5) indicates strong structural tells such as cross-file repetition or cross-linguistic idioms. MEDIUM (2) covers recognisable conversational padding and AI-specific vocabulary. LOW (1) captures subtle indicators like tautological comments and generic boilerplate that require density to carry independent signal.

CRITICAL 0HIGH 488MEDIUM 85LOW 804

Directory Score Breakdown

This horizontal bar chart decomposes the repository's raw synthetic code score by top-level directory, allowing you to pinpoint precisely which modules or components carry the highest AI authorship density. Directories with disproportionately high scores relative to their size warrant targeted manual review: concentrated AI signatures often trace back to mass-generated configuration layers, auto-ported test suites, LLM-scaffolded boilerplate classes, or entire subsystems authored under heavy copilot assistance. Use this view to prioritise your human code-review effort.

Pattern Findings

The scanner identified 1377 distinct pattern matches across 13 syntactic categories. Each entry below represents a discrete location in the source code where the engine recorded a statistically significant AI authorship indicator. Expand any category row to inspect the individual file paths, line numbers, code snippets, and the lexical context (CODE, COMMENT, or STRING) in which each match was detected.

Reading the findings table: The Severity column indicates the diagnostic confidence level (CRITICAL / HIGH / MEDIUM / LOW). The Context column identifies whether the match occurred inside executable code, an inline comment, or a string literal — comment-context matches receive a ×1.5 weight because LLMs systematically over-annotate. The ⚡ bolt icon marks clustered matches: three or more patterns within a 10-line window, each receiving an additional ×1.5 density multiplier as dense clusters constitute far stronger evidence of synthetic authorship than isolated hits.

Cross-File Repetition488 hits · 2440 pts
SeverityFileLineSnippetContext
HIGHrecipes/diatracer/diatracer.py0please provide pass a license key with the --key argument. you may obtain a key by agreeing to the terms at https://msfrSTRING
HIGHrecipes/msfragger/msfragger.py0please provide pass a license key with the --key argument. you may obtain a key by agreeing to the terms at https://msfrSTRING
HIGHrecipes/ionquant/ionquant.py0please provide pass a license key with the --key argument. you may obtain a key by agreeing to the terms at https://msfrSTRING
HIGHrecipes/diatracer/diatracer.py0return the symlink-resolved, canonicalized directory-portion of path.STRING
HIGHrecipes/biotransformer/biotransformer.py0return the symlink-resolved, canonicalized directory-portion of path.STRING
HIGHrecipes/mobster/mobster-to-vcf.py0return the symlink-resolved, canonicalized directory-portion of path.STRING
HIGHrecipes/mobster/mobster.py0return the symlink-resolved, canonicalized directory-portion of path.STRING
HIGHrecipes/biopet-vcfstats/biopet-vcfstats.py0return the symlink-resolved, canonicalized directory-portion of path.STRING
HIGHrecipes/biopet-vcfstats/1.0/biopet-vcfstats.py0return the symlink-resolved, canonicalized directory-portion of path.STRING
HIGHrecipes/biopet-vcfstats/1.1/biopet-vcfstats.py0return the symlink-resolved, canonicalized directory-portion of path.STRING
HIGHrecipes/biopet-vcfstats/1.2/biopet-vcfstats.py0return the symlink-resolved, canonicalized directory-portion of path.STRING
HIGHrecipes/vcf2genome/vcf2genome.py0return the symlink-resolved, canonicalized directory-portion of path.STRING
HIGHrecipes/mpa-server/mpa-server.py0return the symlink-resolved, canonicalized directory-portion of path.STRING
HIGHrecipes/topas/topas.py0return the symlink-resolved, canonicalized directory-portion of path.STRING
HIGHrecipes/biopet-basecounter/biopet-basecounter.py0return the symlink-resolved, canonicalized directory-portion of path.STRING
HIGHrecipes/biopet-basecounter/0.1/biopet-basecounter.py0return the symlink-resolved, canonicalized directory-portion of path.STRING
HIGHrecipes/mgf-formatter/mgf-formatter.py0return the symlink-resolved, canonicalized directory-portion of path.STRING
HIGHrecipes/jmztab-m/jmztab-m.py0return the symlink-resolved, canonicalized directory-portion of path.STRING
HIGHrecipes/biopet-sampleconfig/biopet-sampleconfig.py0return the symlink-resolved, canonicalized directory-portion of path.STRING
HIGHrecipes/biopet-sampleconfig/0.2/biopet-sampleconfig.py0return the symlink-resolved, canonicalized directory-portion of path.STRING
HIGHrecipes/figtree/figtree.py0return the symlink-resolved, canonicalized directory-portion of path.STRING
HIGH…pes/validate-fasta-database/validate-fasta-database.py0return the symlink-resolved, canonicalized directory-portion of path.STRING
HIGH…submission-tool-validator/submission-tool-validator.py0return the symlink-resolved, canonicalized directory-portion of path.STRING
HIGHrecipes/cgview/cgview.py0return the symlink-resolved, canonicalized directory-portion of path.STRING
HIGHrecipes/goenrichment/goenrichment.py0return the symlink-resolved, canonicalized directory-portion of path.STRING
HIGHrecipes/crisper_recognition_tool/crt.py0return the symlink-resolved, canonicalized directory-portion of path.STRING
HIGHrecipes/hap-ibd/hap-ibd.py0return the symlink-resolved, canonicalized directory-portion of path.STRING
HIGHrecipes/hops/MaltExtract.py0return the symlink-resolved, canonicalized directory-portion of path.STRING
HIGHrecipes/hops/hops.py0return the symlink-resolved, canonicalized directory-portion of path.STRING
HIGHrecipes/pepgenome/pepgenome.py0return the symlink-resolved, canonicalized directory-portion of path.STRING
HIGHrecipes/examine/examine.py0return the symlink-resolved, canonicalized directory-portion of path.STRING
HIGHrecipes/sem/sem.py0return the symlink-resolved, canonicalized directory-portion of path.STRING
HIGHrecipes/clinod/clinod.py0return the symlink-resolved, canonicalized directory-portion of path.STRING
HIGHrecipes/biopet-seqstat/biopet-seqstat.py0return the symlink-resolved, canonicalized directory-portion of path.STRING
HIGHrecipes/biopet-seqstat/1.0/biopet-seqstat.py0return the symlink-resolved, canonicalized directory-portion of path.STRING
HIGHrecipes/biopet-seqstat/1.0.1/biopet-seqstat.py0return the symlink-resolved, canonicalized directory-portion of path.STRING
HIGHrecipes/biopet-seqstat/0.1/biopet-seqstat.py0return the symlink-resolved, canonicalized directory-portion of path.STRING
HIGHrecipes/haploview/haploview.py0return the symlink-resolved, canonicalized directory-portion of path.STRING
HIGHrecipes/effectivet3/effectivet3.py0return the symlink-resolved, canonicalized directory-portion of path.STRING
HIGHrecipes/np-likeness-scorer/np-likeness.py0return the symlink-resolved, canonicalized directory-portion of path.STRING
HIGHrecipes/dinosaur/dinosaur.py0return the symlink-resolved, canonicalized directory-portion of path.STRING
HIGHrecipes/biopet-validatefastq/biopet-validatefastq.py0return the symlink-resolved, canonicalized directory-portion of path.STRING
HIGHrecipes/clipandmerge/clipandmerge.py0return the symlink-resolved, canonicalized directory-portion of path.STRING
HIGHrecipes/biopet-bamstats/biopet-bamstats.py0return the symlink-resolved, canonicalized directory-portion of path.STRING
HIGHrecipes/biopet-bamstats/1.0/biopet-bamstats.py0return the symlink-resolved, canonicalized directory-portion of path.STRING
HIGHrecipes/biopet-bamstats/1.0.1/biopet-bamstats.py0return the symlink-resolved, canonicalized directory-portion of path.STRING
HIGH…biopet-validateannotation/biopet-validateannotation.py0return the symlink-resolved, canonicalized directory-portion of path.STRING
HIGHrecipes/msgf_plus/msgf_plus.py0return the symlink-resolved, canonicalized directory-portion of path.STRING
HIGHrecipes/encyclopedia/encyclopedia.py0return the symlink-resolved, canonicalized directory-portion of path.STRING
HIGHrecipes/damageprofiler/damageprofiler.py0return the symlink-resolved, canonicalized directory-portion of path.STRING
HIGHrecipes/searchgui/searchgui.py0return the symlink-resolved, canonicalized directory-portion of path.STRING
HIGHrecipes/snpeff/snpeff.py0return the symlink-resolved, canonicalized directory-portion of path.STRING
HIGHrecipes/snpeff/5.1/snpeff.py0return the symlink-resolved, canonicalized directory-portion of path.STRING
HIGHrecipes/snpeff/5.0/snpeff.py0return the symlink-resolved, canonicalized directory-portion of path.STRING
HIGHrecipes/snpeff/5.1d/snpeff.py0return the symlink-resolved, canonicalized directory-portion of path.STRING
HIGHrecipes/snpeff/4.3.1t/snpeff.py0return the symlink-resolved, canonicalized directory-portion of path.STRING
HIGHrecipes/snpeff/4.5covid19/snpeff.py0return the symlink-resolved, canonicalized directory-portion of path.STRING
HIGHrecipes/snpeff/5.2/snpeff.py0return the symlink-resolved, canonicalized directory-portion of path.STRING
HIGHrecipes/jvarkit-msa2vcf/msa2vcf.py0return the symlink-resolved, canonicalized directory-portion of path.STRING
HIGHrecipes/trimmomatic/trimmomatic.py0return the symlink-resolved, canonicalized directory-portion of path.STRING
428 more matches not shown…
Over-Commented Block599 hits · 509 pts
SeverityFileLineSnippetContext
LOWrecipes/shapeit5/sse2neon.h21 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THECOMMENT
LOWrecipes/shapeit5/sse2neon.h41// Devin Hussey (easyaspi314) <husseydevin@gmail.com>COMMENT
LOWrecipes/shapeit5/sse2neon.h61/* _mm_min|max_ps|ss|pd|sd */COMMENT
LOWrecipes/shapeit5/sse2neon.h81#ifndef SSE2NEON_INCLUDE_WINDOWS_HCOMMENT
LOWrecipes/shapeit5/sse2neon.h101#define ALIGN_STRUCT(x) __declspec(align(x))COMMENT
LOWrecipes/shapeit5/sse2neon.h121#warning "GCC versions earlier than 10 are not supported."COMMENT
LOWrecipes/shapeit5/sse2neon.h141/* If using MSVC */COMMENT
LOWrecipes/shapeit5/sse2neon.h221#else /* MSVC */COMMENT
LOWrecipes/shapeit5/sse2neon.h241#elif defined(__aarch64__) || defined(_M_ARM64)COMMENT
LOWrecipes/shapeit5/sse2neon.h261#include <arm_neon.h>COMMENT
LOWrecipes/shapeit5/sse2neon.h301#define HAS__builtin_popcountll 1COMMENT
LOWrecipes/shapeit5/sse2neon.h341#define vshuffleq_s16(a, b, ...) _sse2neon_shuffle(int16x8_t, a, b, __VA_ARGS__)COMMENT
LOWrecipes/shapeit5/sse2neon.h361#define _MM_FROUND_NEARBYINT (_MM_FROUND_CUR_DIRECTION | _MM_FROUND_NO_EXC)COMMENT
LOWrecipes/shapeit5/sse2neon.h401// __int64 is defined in the Intrinsics Guide which maps to different datatypeCOMMENT
LOWrecipes/shapeit5/sse2neon.h421COMMENT
LOWrecipes/shapeit5/sse2neon.h441#define vreinterpretq_m128i_s8(x) vreinterpretq_s64_s8(x)COMMENT
LOWrecipes/shapeit5/sse2neon.h461#define vreinterpretq_u32_m128i(x) vreinterpretq_u32_s64(x)COMMENT
LOWrecipes/shapeit5/sse2neon.h481#define vreinterpret_u64_m64(x) vreinterpret_u64_s64(x)COMMENT
LOWrecipes/shapeit5/sse2neon.h501#define vreinterpretq_u32_m128d(x) vreinterpretq_u32_f64(x)COMMENT
LOWrecipes/shapeit5/sse2neon.h521#endifCOMMENT
LOWrecipes/shapeit5/sse2neon.h881 return vreinterpretq_u64_p128(vmull_p64(a, b));COMMENT
LOWrecipes/shapeit5/sse2neon.h981COMMENT
LOWrecipes/shapeit5/sse2neon.h1101#endifCOMMENT
LOWrecipes/shapeit5/sse2neon.h1401// Compare the lower single-precision (32-bit) floating-point elements in a andCOMMENT
LOWrecipes/shapeit5/sse2neon.h1621COMMENT
LOWrecipes/shapeit5/sse2neon.h1721COMMENT
LOWrecipes/shapeit5/sse2neon.h1861 vreinterpret_m64_s16(vset_lane_s16((b), vreinterpret_s16_m64(a), (imm)))COMMENT
LOWrecipes/shapeit5/sse2neon.h2201// Compute the bitwise OR of packed single-precision (32-bit) floating-pointCOMMENT
LOWrecipes/shapeit5/sse2neon.h2221// the lower element of dst.COMMENT
LOWrecipes/shapeit5/sse2neon.h2241// values in dst.COMMENT
LOWrecipes/shapeit5/sse2neon.h2301// b, then horizontally sum each consecutive 8 differences to produce fourCOMMENT
LOWrecipes/shapeit5/sse2neon.h2321 // Additional Netwon-Raphson iteration for accuracyCOMMENT
LOWrecipes/shapeit5/sse2neon.h2561 _sse2neon_return(vreinterpret_m64_s16(ret));)COMMENT
LOWrecipes/shapeit5/sse2neon.h2741// Store the lower single-precision (32-bit) floating-point element from a intoCOMMENT
LOWrecipes/shapeit5/sse2neon.h2861#define _mm_ucomilt_ss _mm_comilt_ssCOMMENT
LOWrecipes/shapeit5/sse2neon.h2881COMMENT
LOWrecipes/shapeit5/sse2neon.h3101COMMENT
LOWrecipes/shapeit5/sse2neon.h3901// Convert packed signed 32-bit integers in a to packed double-precisionCOMMENT
LOWrecipes/shapeit5/sse2neon.h4021#elseCOMMENT
LOWrecipes/shapeit5/sse2neon.h4081#endifCOMMENT
LOWrecipes/shapeit5/sse2neon.h4121// element.COMMENT
LOWrecipes/shapeit5/sse2neon.h4241// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_extract_epi16COMMENT
LOWrecipes/shapeit5/sse2neon.h4261#if defined(__aarch64__) || defined(_M_ARM64)COMMENT
LOWrecipes/shapeit5/sse2neon.h4561// of dst.COMMENT
LOWrecipes/shapeit5/sse2neon.h4581COMMENT
LOWrecipes/shapeit5/sse2neon.h4601 // Merge the even lanes together with a 16-bit unsigned shift right + add.COMMENT
LOWrecipes/shapeit5/sse2neon.h4621 // \| \|COMMENT
LOWrecipes/shapeit5/sse2neon.h4921// Set packed double-precision (64-bit) floating-point elements in dst with theCOMMENT
LOWrecipes/shapeit5/sse2neon.h5441// elements) from a into memory. mem_addr must be aligned on a 16-byte boundaryCOMMENT
LOWrecipes/shapeit5/sse2neon.h5481COMMENT
LOWrecipes/shapeit5/sse2neon.h5561COMMENT
LOWrecipes/shapeit5/sse2neon.h5721#define _mm_ucomile_sd _mm_comile_sdCOMMENT
LOWrecipes/shapeit5/sse2neon.h5921// Alternatively add and subtract packed double-precision (64-bit)COMMENT
LOWrecipes/shapeit5/sse2neon.h6021COMMENT
LOWrecipes/shapeit5/sse2neon.h6801COMMENT
LOWrecipes/shapeit5/sse2neon.h7081// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_extract_epi64COMMENT
LOWrecipes/shapeit5/sse2neon.h7121 return _mm_set_ps(floorf(f[3]), floorf(f[2]), floorf(f[1]), floorf(f[0]));COMMENT
LOWrecipes/shapeit5/sse2neon.h7141{COMMENT
LOWrecipes/shapeit5/sse2neon.h7161 vsetq_lane_s64((b), vreinterpretq_s64_m128i(a), (imm)))COMMENT
LOWrecipes/shapeit5/sse2neon.h7561// the rounding parameter, store the result as a double-precision floating-pointCOMMENT
539 more matches not shown…
Deep Nesting133 hits · 133 pts
SeverityFileLineSnippetContext
LOWrecipes/diatracer/diatracer.py36CODE
LOWrecipes/biotransformer/biotransformer.py41CODE
LOWrecipes/mobster/mobster-to-vcf.py39CODE
LOWrecipes/mobster/mobster.py39CODE
LOWrecipes/biopet-vcfstats/biopet-vcfstats.py43CODE
LOWrecipes/biopet-vcfstats/1.0/biopet-vcfstats.py43CODE
LOWrecipes/biopet-vcfstats/1.1/biopet-vcfstats.py43CODE
LOWrecipes/biopet-vcfstats/1.2/biopet-vcfstats.py43CODE
LOWrecipes/vcf2genome/vcf2genome.py36CODE
LOWrecipes/mpa-server/mpa-server.py51CODE
LOWrecipes/mpa-server/mpa-server.py97CODE
LOWrecipes/mpa-server/mpa-server.py116CODE
LOWrecipes/mpa-server/mpa-server.py162CODE
LOWrecipes/topas/topas.py36CODE
LOWrecipes/biopet-basecounter/biopet-basecounter.py43CODE
LOWrecipes/biopet-basecounter/0.1/biopet-basecounter.py43CODE
LOWrecipes/mgf-formatter/mgf-formatter.py36CODE
LOWrecipes/jmztab-m/jmztab-m.py42CODE
LOWrecipes/biopet-sampleconfig/biopet-sampleconfig.py43CODE
LOWrecipes/biopet-sampleconfig/0.2/biopet-sampleconfig.py43CODE
LOWrecipes/figtree/figtree.py41CODE
LOW…pes/validate-fasta-database/validate-fasta-database.py39CODE
LOW…submission-tool-validator/submission-tool-validator.py41CODE
LOWrecipes/cgview/cgview.py39CODE
LOWrecipes/goenrichment/goenrichment.py41CODE
LOWrecipes/hap-ibd/hap-ibd.py41CODE
LOWrecipes/hops/MaltExtract.py36CODE
LOWrecipes/hops/hops.py36CODE
LOWrecipes/pepgenome/pepgenome.py38CODE
LOWrecipes/examine/examine.py41CODE
LOWrecipes/bioconda-repodata-patches/gen_patch_json.py88CODE
LOWrecipes/sem/sem.py40CODE
LOWrecipes/clinod/clinod.py39CODE
LOWrecipes/biopet-seqstat/biopet-seqstat.py43CODE
LOWrecipes/biopet-seqstat/1.0/biopet-seqstat.py43CODE
LOWrecipes/biopet-seqstat/1.0.1/biopet-seqstat.py43CODE
LOWrecipes/biopet-seqstat/0.1/biopet-seqstat.py43CODE
LOWrecipes/haploview/haploview.py39CODE
LOWrecipes/effectivet3/effectivet3.py39CODE
LOWrecipes/dinosaur/dinosaur.py37CODE
LOWrecipes/biopet-validatefastq/biopet-validatefastq.py43CODE
LOWrecipes/clipandmerge/clipandmerge.py36CODE
LOWrecipes/biopet-bamstats/biopet-bamstats.py43CODE
LOWrecipes/biopet-bamstats/1.0/biopet-bamstats.py43CODE
LOWrecipes/biopet-bamstats/1.0.1/biopet-bamstats.py43CODE
LOW…biopet-validateannotation/biopet-validateannotation.py43CODE
LOWrecipes/msgf_plus/msgf_plus.py36CODE
LOWrecipes/encyclopedia/encyclopedia.py41CODE
LOWrecipes/damageprofiler/damageprofiler.py36CODE
LOWrecipes/searchgui/searchgui.py40CODE
LOWrecipes/snpeff/snpeff.py45CODE
LOWrecipes/snpeff/5.1/snpeff.py41CODE
LOWrecipes/snpeff/5.0/snpeff.py41CODE
LOWrecipes/snpeff/5.1d/snpeff.py41CODE
LOWrecipes/snpeff/4.3.1t/snpeff.py41CODE
LOWrecipes/snpeff/4.5covid19/snpeff.py41CODE
LOWrecipes/snpeff/5.2/snpeff.py45CODE
LOWrecipes/jvarkit-msa2vcf/msa2vcf.py41CODE
LOWrecipes/trimmomatic/trimmomatic.py40CODE
LOWrecipes/trimmomatic/0.39/trimmomatic.py40CODE
73 more matches not shown…
Self-Referential Comments42 hits · 130 pts
SeverityFileLineSnippetContext
MEDIUMrecipes/muset/build.sh13# Create the output directoryCOMMENT
MEDIUMrecipes/genera/build.sh9# Define the Conda binary pathCOMMENT
MEDIUMrecipes/ciri2/build.sh4# Create a binary directory in conda environmentCOMMENT
MEDIUMrecipes/sqanti3/build.sh4# Define the isolated share directory for this specific versionCOMMENT
MEDIUMrecipes/sqanti3/build.sh7# Create the necessary directoriesCOMMENT
MEDIUMrecipes/fungar/build.sh4# Create the bin directory for executable scriptsCOMMENT
MEDIUMrecipes/fungar/build.sh7# Create the directory for the databaseCOMMENT
MEDIUMrecipes/sipros/build.sh37# Create the siproswf scriptCOMMENT
MEDIUMrecipes/sipros/build.sh44# Create the link of extractPro.shCOMMENT
MEDIUMrecipes/wepp/build.sh71# Create the wrapper scriptCOMMENT
MEDIUMrecipes/bramble/build.sh24# Create a symbolic link so both `bramble` and `bramble-rs` workCOMMENT
MEDIUMrecipes/digest/build.sh54# Create the Python package directory if it doesn't existCOMMENT
MEDIUMrecipes/ciri-full/build.sh9# Create a wrapper script to run the jar fileCOMMENT
MEDIUMrecipes/longreadsum/build.sh14# Create the src directoryCOMMENT
MEDIUMrecipes/clincnv/build.sh13 # Define the wrapper script pathCOMMENT
MEDIUMrecipes/clincnv/build.sh16 # Create the wrapper scriptCOMMENT
MEDIUMrecipes/cats-rb/build.sh3#Creating the bin directoryCOMMENT
MEDIUMrecipes/atlas-fastq-provider/build.sh6# Create a config if not already presentCOMMENT
MEDIUMrecipes/tncomp_finder/build.sh3# Create the destination directoryCOMMENT
MEDIUMrecipes/tncomp_finder/build.sh15# Create a wrapper script in binCOMMENT
MEDIUMrecipes/metawepp/build.sh10# Create the wrapper scriptCOMMENT
MEDIUMrecipes/tn3_ta_finder/build.sh3# Create the destination directoryCOMMENT
MEDIUMrecipes/tn3_ta_finder/build.sh15# Create a wrapper script in binCOMMENT
MEDIUMrecipes/translatory/build.sh3# Create the binary directory in the Conda environmentCOMMENT
MEDIUMrecipes/redundans/build.sh3#Define the install folder and binary folder and create themCOMMENT
MEDIUMrecipes/netmd/build.sh3# This file is part of the Karate Club package.COMMENT
MEDIUMrecipes/cctyper/post-link.sh6## Create a folder in the conda directory to host these files ("cct_data")COMMENT
MEDIUMrecipes/gzrt/build.sh27 # Create a temporary directoryCOMMENT
MEDIUMrecipes/gzrt/build.sh30 # Create a symlink named cc that points to $CCCOMMENT
MEDIUMrecipes/unifire/build.sh67# Create a wrapper to invoke it with pythonCOMMENT
MEDIUMrecipes/absense/build.sh12# Define the Conda binary pathCOMMENT
MEDIUMrecipes/corona_lineage_dynamics/build.sh5# Define the target directoryCOMMENT
MEDIUMrecipes/corona_lineage_dynamics/build.sh8# Create the target directoryCOMMENT
MEDIUMrecipes/corona_lineage_dynamics/build.sh14# Create the proxy script in $PREFIX/binCOMMENT
MEDIUMrecipes/jacusa2/build.sh3# Create the installation directoryCOMMENT
MEDIUMrecipes/jacusa2/build.sh9# Create a wrapper script named "JACUSA2" so users can run the jar directlyCOMMENT
MEDIUMrecipes/neptune-signature/post-link.sh15# Creating a new executable (while preserving permissions). The new executableCOMMENT
MEDIUMrecipes/acedrg/build.sh24# Create a symlink for libmol if the upstream build installs it under libexecCOMMENT
MEDIUMrecipes/pybigtools/build.sh26# Creating the sdist from the monorepo placed pyproject.toml one level above Cargo.toml.COMMENT
MEDIUMrecipes/cats-rf/build.sh3#Creating the bin directoryCOMMENT
MEDIUMrecipes/haplink/build.sh33# Create a permanent depotCOMMENT
MEDIUMrecipes/hifiadapterfilt/build.sh14# Create an activation script for BiocondaCOMMENT
Decorative Section Separators25 hits · 99 pts
SeverityFileLineSnippetContext
MEDIUMrecipes/altair-mf/meta.yaml3# ------------------------------------------------COMMENT
MEDIUMrecipes/ltr_retriever/build.sh10# -----------------COMMENT
MEDIUMrecipes/ltr_retriever/build.sh21# -----------------COMMENT
MEDIUMrecipes/phageflow/meta.yaml34 # ── QC ───────────────────────────────────────────────────────────────────COMMENT
MEDIUMrecipes/phageflow/meta.yaml38 # ── Host removal ─────────────────────────────────────────────────────────COMMENT
MEDIUMrecipes/phageflow/meta.yaml44 # ── Assembly ─────────────────────────────────────────────────────────────COMMENT
MEDIUMrecipes/phageflow/meta.yaml48 # ── Coverage ─────────────────────────────────────────────────────────────COMMENT
MEDIUMrecipes/phageflow/meta.yaml50 # ── Viral ID ─────────────────────────────────────────────────────────────COMMENT
MEDIUMrecipes/phageflow/meta.yaml52 # ── Quality ──────────────────────────────────────────────────────────────COMMENT
MEDIUMrecipes/phageflow/meta.yaml57 # ── Annotation ───────────────────────────────────────────────────────────COMMENT
MEDIUMrecipes/themis/build.sh11# -----------------------------------------------------------------------------COMMENT
MEDIUMrecipes/themis/build.sh26# -----------------------------------------------------------------------------COMMENT
MEDIUMrecipes/themis/build.sh41# -----------------------------------------------------------------------------COMMENT
MEDIUMrecipes/themis/build.sh48# -----------------------------------------------------------------------------COMMENT
MEDIUMrecipes/themis/build.sh49# -----------------------------------------------------------------------------COMMENT
MEDIUMrecipes/themis/build.sh51# -----------------------------------------------------------------------------COMMENT
MEDIUMrecipes/themis/build.sh52# -----------------------------------------------------------------------------COMMENT
MEDIUMrecipes/csem/build.sh4# --------------------------------------------------------------------------COMMENT
MEDIUMrecipes/csem/build.sh13# --------------------------------------------------------------------------COMMENT
MEDIUMrecipes/unifire/post-link.sh18# ------------------------------------------------------------COMMENT
MEDIUMrecipes/unifire/post-link.sh20# ------------------------------------------------------------COMMENT
MEDIUMrecipes/unifire/post-link.sh37# ------------------------------------------------------------COMMENT
MEDIUMrecipes/unifire/post-link.sh39# ------------------------------------------------------------COMMENT
MEDIUMrecipes/unifire/post-link.sh44# ------------------------------------------------------------COMMENT
MEDIUMrecipes/unifire/post-link.sh46# ------------------------------------------------------------COMMENT
Redundant / Tautological Comments28 hits · 42 pts
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LOWrecipes/sfold/meta.yaml30 - sfold -h # Check if sfold command runs successfullyCODE
LOWrecipes/qualimap/build.sh13# Set QUALIMAP_HOME to libraries path. This can help qualimap know where scripts/ forlder is.COMMENT
LOWrecipes/qualimap/build.sh15# Set classpath to librariesCOMMENT
LOWrecipes/qualimap/2.1.1/build.sh13# Set QUALIMAP_HOME to libraries path. This can help qualimap know where scripts/ forlder is.COMMENT
LOWrecipes/qualimap/2.1.1/build.sh15# Set classpath to librariesCOMMENT
LOWrecipes/qualimap/2.2.2c/build.sh13# Set QUALIMAP_HOME to libraries path. This can help qualimap know where scripts/ forlder is.COMMENT
LOWrecipes/qualimap/2.2.2c/build.sh15# Set classpath to librariesCOMMENT
LOWrecipes/gtdbtk/download-db.sh47# Check if this is overriding an existing versionCOMMENT
LOWrecipes/b2btools/.run_test.sh47 # Check if the status code is non-zero and exit with an error codeCOMMENT
LOWrecipes/b2btools/.run_test.sh61 # Check if the file is a CSV and has more than one rowCOMMENT
LOWrecipes/b2btools/.run_test.sh90 # Check if the status code is non-zero and exit with an error codeCOMMENT
LOWrecipes/b2btools/.run_test.sh104 # Check if the file is a CSV and has more than one rowCOMMENT
LOWrecipes/b2btools/.run_test.sh133 # Check if the status code is non-zero and exit with an error codeCOMMENT
LOWrecipes/b2btools/.run_test.sh147 # Check if the file is a CSV and has more than one rowCOMMENT
LOWrecipes/b2btools/.run_test.sh182 # Check if the status code is non-zero and exit with an error codeCOMMENT
LOWrecipes/b2btools/.run_test.sh196 # Check if the file is a CSV and has more than one rowCOMMENT
LOWrecipes/b2btools/.run_test.sh229 # Check if the status code is non-zero and exit with an error codeCOMMENT
LOWrecipes/b2btools/.run_test.sh243 # Check if the file is a CSV and has more than one rowCOMMENT
LOWrecipes/b2btools/.run_test.sh274 # Check if the status code is non-zero and exit with an error codeCOMMENT
LOWrecipes/b2btools/.run_test.sh288 # Check if the file is a CSV and has more than one rowCOMMENT
LOWrecipes/mango/post-link.sh3# Set SPARK_HOME to conda installed pyspark package if not already setCOMMENT
LOWrecipes/mango/activate.sh3# Set SPARK_HOME to conda installed pyspark package if not already setCOMMENT
LOWrecipes/earlgrey/build.sh47# Set permissions to filesCOMMENT
LOWrecipes/pyopenms/build.sh24# Set INSTALL_RPATH to PREFIX such that there are no warnings during linkage fixing of conda-buildCOMMENT
LOWrecipes/minimac4/build.sh6# Set CXXFLAGS to include the correct path to lzma.h and LDFLAGS to include the path to liblzmaCOMMENT
LOWrecipes/haddock_biobb/post-link.sh3# Check if gcc is available. As gcc is hardcoded in haddock3 setup.py, it's unavailable on Bioconda tests.COMMENT
LOWrecipes/openms-meta/build.sh24# Set INSTALL_RPATH to PREFIX such that there are no warnings during linkage fixing of conda-buildCOMMENT
LOWscripts/check-for-additional-platforms.sh45 # Check if any additional platforms match this jobCOMMENT
Unused Imports33 hits · 33 pts
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LOWrecipes/biotransformer/biotransformer.py12CODE
LOWrecipes/crisper_recognition_tool/crt.py12CODE
LOWrecipes/pyopt/run_test.py2CODE
LOWrecipes/pyopt/run_test.py3CODE
LOWrecipes/pyopt/run_test.py4CODE
LOWrecipes/pyopt/run_test.py5CODE
LOWrecipes/pyopt/run_test.py6CODE
LOWrecipes/pyopt/run_test.py7CODE
LOWrecipes/pyopt/run_test.py8CODE
LOWrecipes/pyopt/run_test.py9CODE
LOWrecipes/pyopt/run_test.py10CODE
LOWrecipes/pyopt/run_test.py11CODE
LOWrecipes/pyopt/run_test.py12CODE
LOWrecipes/pyopt/run_test.py13CODE
LOWrecipes/pyopt/run_test.py14CODE
LOWrecipes/bioconda-repodata-patches/gen_patch_json.py3CODE
LOWrecipes/bioconda-repodata-patches/gen_patch_json.py3CODE
LOWrecipes/bioconda-repodata-patches/gen_patch_json.py3CODE
LOWrecipes/np-likeness-scorer/np-likeness.py12CODE
LOWrecipes/transabyss/setup.py1CODE
LOWrecipes/transabyss/setup.py2CODE
LOWrecipes/transabyss/setup.py2CODE
LOWrecipes/mango/run_test.py2CODE
LOWrecipes/mango/run_test.py3CODE
LOWrecipes/mango/run_test.py4CODE
LOWrecipes/mango/run_test.py5CODE
LOWrecipes/mango/run_test.py6CODE
LOWrecipes/fseq/fseq.py14CODE
LOWrecipes/fseq/fseq.py18CODE
LOW…cipes/jvarkit-wgscoverageplotter/wgscoverageplotter.py12CODE
LOWrecipes/pysam/run_test.py1CODE
LOWrecipes/gemoma/GeMoMa.py12CODE
LOWrecipes/bamr/run_test.py1CODE
AI Slop Vocabulary10 hits · 22 pts
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LOWrecipes/cactus/build.sh45# cactus-gfa-tools is required but doesn't have tags. They just use exact commits in their scriptsCOMMENT
MEDIUMrecipes/bioconductor-visiumstitched/meta.yaml80 description: This package provides helper functions for working with multiple Visium capture areas that overlap each oCODE
MEDIUMrecipes/r-genekitr/meta.yaml95# Description: Provides features for searching, converting, analyzing, plotting, and exporting data effortlessly by inpuCOMMENT
MEDIUMrecipes/delve-bio/meta.yaml9 url: https://github.com/berndbohmeier/delve/archive/v{{ version }}.tar.gzCODE
MEDIUMrecipes/delve-bio/meta.yaml34 home: https://github.com/berndbohmeier/delveCODE
MEDIUMrecipes/bwa-mem3/build.sh80 # bundled MI_OVERRIDE=ON libmimalloc.a is the only robust override on Linux,COMMENT
MEDIUMrecipes/tapestry/meta.yaml8 url: https://github.com/johnomics/tapestry/archive/v{{ version}}.tar.gzCODE
MEDIUMrecipes/tapestry/meta.yaml38 home: https://github.com/johnomics/tapestryCODE
MEDIUMrecipes/tapestry/meta.yaml43 dev_url: https://github.com/johnomics/tapestryCODE
MEDIUMrecipes/enzywizard-energy/meta.yaml41 # OpenMM can leverage CUDA if available in the environment.COMMENT
Slop Phrases9 hits · 17 pts
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MEDIUMrecipes/bioconductor-breakpointrdata/meta.yaml36 summary: Strand-seq data for demonstration purposesCODE
LOWrecipes/mccortex/run_test.sh9# let's make sure to check both k-mer sizes were compiledCOMMENT
MEDIUMrecipes/bioconductor-aneufinderdata/meta.yaml35 summary: WGSCS Data for Demonstration PurposesCODE
MEDIUMrecipes/bioconductor-aneufinderdata/meta.yaml36 description: Whole-genome single cell sequencing data for demonstration purposes in the AneuFinder package.CODE
MEDIUMrecipes/bioconductor-targetsearchdata/meta.yaml36 description: Example files of GC-MS data for the TargetSearch Package. The package contains raw NetCDF files from a E.CODE
MEDIUMrecipes/bioconductor-chromstardata/meta.yaml35 summary: ChIP-seq data for Demonstration PurposesCODE
MEDIUMrecipes/bioconductor-chromstardata/meta.yaml36 description: ChIP-seq data for demonstration purposes in the chromstaR package.CODE
MEDIUMrecipes/bioconductor-prebsdata/meta.yaml36 description: 'This package contains data required to run examples in ''prebs'' package. The data files include: 1) SmaCODE
LOWrecipes/optitype/config.ini11# environment OptiType is run, so make sure to include it in PATH.COMMENT
Hyper-Verbose Identifiers6 hits · 6 pts
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LOWrecipes/mpa-server/mpa-server.py198def prompt_user_for_data_download():CODE
LOWrecipes/needletail/run_test.py22 def test_can_parse_fasta_file(self):CODE
LOWrecipes/needletail/run_test.py41 def test_can_parse_fastq_file(self):CODE
LOWrecipes/pycoverm/run_test.py17 def test_get_coverages_from_bam(self):CODE
LOWrecipes/bioconda-repodata-patches/gen_patch_json.py53def _gen_patch_instructions_per_key(index_per_key, new_index, subdir):CODE
LOWrecipes/bioconda-repodata-patches/show_diff.py21def show_record_diffs_per_key(packages_key, subdir, ref_repodata, new_repodata):CODE
Excessive Try-Catch Wrapping2 hits · 3 pts
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MEDIUMrecipes/ena-webin-cli/ena_webin_cli.py122 print(f"Error: failed to exec java: {e}", file=sys.stderr)CODE
LOWrecipes/ega-cryptor/ega-cryptor.py106 except Exception as e:CODE
Modern AI Meta-Vocabulary1 hit · 3 pts
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MEDIUMrecipes/enzywizard-batch/meta.yaml52 # Note: This is a meta-workflow tool that orchestrates many EnzyWizard components.COMMENT
Example Usage Blocks1 hit · 2 pts
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LOWrecipes/verifybamid2/verifybamid2.sh5# Usage:COMMENT