Conda recipes for the bioconda channel.
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).
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.
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.
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.
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.
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| HIGH | recipes/diatracer/diatracer.py | 0 | please provide pass a license key with the --key argument. you may obtain a key by agreeing to the terms at https://msfr | STRING |
| HIGH | recipes/msfragger/msfragger.py | 0 | please provide pass a license key with the --key argument. you may obtain a key by agreeing to the terms at https://msfr | STRING |
| HIGH | recipes/ionquant/ionquant.py | 0 | please provide pass a license key with the --key argument. you may obtain a key by agreeing to the terms at https://msfr | STRING |
| HIGH | recipes/diatracer/diatracer.py | 0 | return the symlink-resolved, canonicalized directory-portion of path. | STRING |
| HIGH | recipes/biotransformer/biotransformer.py | 0 | return the symlink-resolved, canonicalized directory-portion of path. | STRING |
| HIGH | recipes/mobster/mobster-to-vcf.py | 0 | return the symlink-resolved, canonicalized directory-portion of path. | STRING |
| HIGH | recipes/mobster/mobster.py | 0 | return the symlink-resolved, canonicalized directory-portion of path. | STRING |
| HIGH | recipes/biopet-vcfstats/biopet-vcfstats.py | 0 | return the symlink-resolved, canonicalized directory-portion of path. | STRING |
| HIGH | recipes/biopet-vcfstats/1.0/biopet-vcfstats.py | 0 | return the symlink-resolved, canonicalized directory-portion of path. | STRING |
| HIGH | recipes/biopet-vcfstats/1.1/biopet-vcfstats.py | 0 | return the symlink-resolved, canonicalized directory-portion of path. | STRING |
| HIGH | recipes/biopet-vcfstats/1.2/biopet-vcfstats.py | 0 | return the symlink-resolved, canonicalized directory-portion of path. | STRING |
| HIGH | recipes/vcf2genome/vcf2genome.py | 0 | return the symlink-resolved, canonicalized directory-portion of path. | STRING |
| HIGH | recipes/mpa-server/mpa-server.py | 0 | return the symlink-resolved, canonicalized directory-portion of path. | STRING |
| HIGH | recipes/topas/topas.py | 0 | return the symlink-resolved, canonicalized directory-portion of path. | STRING |
| HIGH | recipes/biopet-basecounter/biopet-basecounter.py | 0 | return the symlink-resolved, canonicalized directory-portion of path. | STRING |
| HIGH | recipes/biopet-basecounter/0.1/biopet-basecounter.py | 0 | return the symlink-resolved, canonicalized directory-portion of path. | STRING |
| HIGH | recipes/mgf-formatter/mgf-formatter.py | 0 | return the symlink-resolved, canonicalized directory-portion of path. | STRING |
| HIGH | recipes/jmztab-m/jmztab-m.py | 0 | return the symlink-resolved, canonicalized directory-portion of path. | STRING |
| HIGH | recipes/biopet-sampleconfig/biopet-sampleconfig.py | 0 | return the symlink-resolved, canonicalized directory-portion of path. | STRING |
| HIGH | recipes/biopet-sampleconfig/0.2/biopet-sampleconfig.py | 0 | return the symlink-resolved, canonicalized directory-portion of path. | STRING |
| HIGH | recipes/figtree/figtree.py | 0 | return the symlink-resolved, canonicalized directory-portion of path. | STRING |
| HIGH | …pes/validate-fasta-database/validate-fasta-database.py | 0 | return the symlink-resolved, canonicalized directory-portion of path. | STRING |
| HIGH | …submission-tool-validator/submission-tool-validator.py | 0 | return the symlink-resolved, canonicalized directory-portion of path. | STRING |
| HIGH | recipes/cgview/cgview.py | 0 | return the symlink-resolved, canonicalized directory-portion of path. | STRING |
| HIGH | recipes/goenrichment/goenrichment.py | 0 | return the symlink-resolved, canonicalized directory-portion of path. | STRING |
| HIGH | recipes/crisper_recognition_tool/crt.py | 0 | return the symlink-resolved, canonicalized directory-portion of path. | STRING |
| HIGH | recipes/hap-ibd/hap-ibd.py | 0 | return the symlink-resolved, canonicalized directory-portion of path. | STRING |
| HIGH | recipes/hops/MaltExtract.py | 0 | return the symlink-resolved, canonicalized directory-portion of path. | STRING |
| HIGH | recipes/hops/hops.py | 0 | return the symlink-resolved, canonicalized directory-portion of path. | STRING |
| HIGH | recipes/pepgenome/pepgenome.py | 0 | return the symlink-resolved, canonicalized directory-portion of path. | STRING |
| HIGH | recipes/examine/examine.py | 0 | return the symlink-resolved, canonicalized directory-portion of path. | STRING |
| HIGH | recipes/sem/sem.py | 0 | return the symlink-resolved, canonicalized directory-portion of path. | STRING |
| HIGH | recipes/clinod/clinod.py | 0 | return the symlink-resolved, canonicalized directory-portion of path. | STRING |
| HIGH | recipes/biopet-seqstat/biopet-seqstat.py | 0 | return the symlink-resolved, canonicalized directory-portion of path. | STRING |
| HIGH | recipes/biopet-seqstat/1.0/biopet-seqstat.py | 0 | return the symlink-resolved, canonicalized directory-portion of path. | STRING |
| HIGH | recipes/biopet-seqstat/1.0.1/biopet-seqstat.py | 0 | return the symlink-resolved, canonicalized directory-portion of path. | STRING |
| HIGH | recipes/biopet-seqstat/0.1/biopet-seqstat.py | 0 | return the symlink-resolved, canonicalized directory-portion of path. | STRING |
| HIGH | recipes/haploview/haploview.py | 0 | return the symlink-resolved, canonicalized directory-portion of path. | STRING |
| HIGH | recipes/effectivet3/effectivet3.py | 0 | return the symlink-resolved, canonicalized directory-portion of path. | STRING |
| HIGH | recipes/np-likeness-scorer/np-likeness.py | 0 | return the symlink-resolved, canonicalized directory-portion of path. | STRING |
| HIGH | recipes/dinosaur/dinosaur.py | 0 | return the symlink-resolved, canonicalized directory-portion of path. | STRING |
| HIGH | recipes/biopet-validatefastq/biopet-validatefastq.py | 0 | return the symlink-resolved, canonicalized directory-portion of path. | STRING |
| HIGH | recipes/clipandmerge/clipandmerge.py | 0 | return the symlink-resolved, canonicalized directory-portion of path. | STRING |
| HIGH | recipes/biopet-bamstats/biopet-bamstats.py | 0 | return the symlink-resolved, canonicalized directory-portion of path. | STRING |
| HIGH | recipes/biopet-bamstats/1.0/biopet-bamstats.py | 0 | return the symlink-resolved, canonicalized directory-portion of path. | STRING |
| HIGH | recipes/biopet-bamstats/1.0.1/biopet-bamstats.py | 0 | return the symlink-resolved, canonicalized directory-portion of path. | STRING |
| HIGH | …biopet-validateannotation/biopet-validateannotation.py | 0 | return the symlink-resolved, canonicalized directory-portion of path. | STRING |
| HIGH | recipes/msgf_plus/msgf_plus.py | 0 | return the symlink-resolved, canonicalized directory-portion of path. | STRING |
| HIGH | recipes/encyclopedia/encyclopedia.py | 0 | return the symlink-resolved, canonicalized directory-portion of path. | STRING |
| HIGH | recipes/damageprofiler/damageprofiler.py | 0 | return the symlink-resolved, canonicalized directory-portion of path. | STRING |
| HIGH | recipes/searchgui/searchgui.py | 0 | return the symlink-resolved, canonicalized directory-portion of path. | STRING |
| HIGH | recipes/snpeff/snpeff.py | 0 | return the symlink-resolved, canonicalized directory-portion of path. | STRING |
| HIGH | recipes/snpeff/5.1/snpeff.py | 0 | return the symlink-resolved, canonicalized directory-portion of path. | STRING |
| HIGH | recipes/snpeff/5.0/snpeff.py | 0 | return the symlink-resolved, canonicalized directory-portion of path. | STRING |
| HIGH | recipes/snpeff/5.1d/snpeff.py | 0 | return the symlink-resolved, canonicalized directory-portion of path. | STRING |
| HIGH | recipes/snpeff/4.3.1t/snpeff.py | 0 | return the symlink-resolved, canonicalized directory-portion of path. | STRING |
| HIGH | recipes/snpeff/4.5covid19/snpeff.py | 0 | return the symlink-resolved, canonicalized directory-portion of path. | STRING |
| HIGH | recipes/snpeff/5.2/snpeff.py | 0 | return the symlink-resolved, canonicalized directory-portion of path. | STRING |
| HIGH | recipes/jvarkit-msa2vcf/msa2vcf.py | 0 | return the symlink-resolved, canonicalized directory-portion of path. | STRING |
| HIGH | recipes/trimmomatic/trimmomatic.py | 0 | return the symlink-resolved, canonicalized directory-portion of path. | STRING |
| 428 more matches not shown… | ||||
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | recipes/shapeit5/sse2neon.h | 21 | * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | COMMENT |
| LOW | recipes/shapeit5/sse2neon.h | 41 | // Devin Hussey (easyaspi314) <husseydevin@gmail.com> | COMMENT |
| LOW | recipes/shapeit5/sse2neon.h | 61 | /* _mm_min|max_ps|ss|pd|sd */ | COMMENT |
| LOW | recipes/shapeit5/sse2neon.h | 81 | #ifndef SSE2NEON_INCLUDE_WINDOWS_H | COMMENT |
| LOW | recipes/shapeit5/sse2neon.h | 101 | #define ALIGN_STRUCT(x) __declspec(align(x)) | COMMENT |
| LOW | recipes/shapeit5/sse2neon.h | 121 | #warning "GCC versions earlier than 10 are not supported." | COMMENT |
| LOW | recipes/shapeit5/sse2neon.h | 141 | /* If using MSVC */ | COMMENT |
| LOW | recipes/shapeit5/sse2neon.h | 221 | #else /* MSVC */ | COMMENT |
| LOW | recipes/shapeit5/sse2neon.h | 241 | #elif defined(__aarch64__) || defined(_M_ARM64) | COMMENT |
| LOW | recipes/shapeit5/sse2neon.h | 261 | #include <arm_neon.h> | COMMENT |
| LOW | recipes/shapeit5/sse2neon.h | 301 | #define HAS__builtin_popcountll 1 | COMMENT |
| LOW | recipes/shapeit5/sse2neon.h | 341 | #define vshuffleq_s16(a, b, ...) _sse2neon_shuffle(int16x8_t, a, b, __VA_ARGS__) | COMMENT |
| LOW | recipes/shapeit5/sse2neon.h | 361 | #define _MM_FROUND_NEARBYINT (_MM_FROUND_CUR_DIRECTION | _MM_FROUND_NO_EXC) | COMMENT |
| LOW | recipes/shapeit5/sse2neon.h | 401 | // __int64 is defined in the Intrinsics Guide which maps to different datatype | COMMENT |
| LOW | recipes/shapeit5/sse2neon.h | 421 | COMMENT | |
| LOW | recipes/shapeit5/sse2neon.h | 441 | #define vreinterpretq_m128i_s8(x) vreinterpretq_s64_s8(x) | COMMENT |
| LOW | recipes/shapeit5/sse2neon.h | 461 | #define vreinterpretq_u32_m128i(x) vreinterpretq_u32_s64(x) | COMMENT |
| LOW | recipes/shapeit5/sse2neon.h | 481 | #define vreinterpret_u64_m64(x) vreinterpret_u64_s64(x) | COMMENT |
| LOW | recipes/shapeit5/sse2neon.h | 501 | #define vreinterpretq_u32_m128d(x) vreinterpretq_u32_f64(x) | COMMENT |
| LOW | recipes/shapeit5/sse2neon.h | 521 | #endif | COMMENT |
| LOW | recipes/shapeit5/sse2neon.h | 881 | return vreinterpretq_u64_p128(vmull_p64(a, b)); | COMMENT |
| LOW | recipes/shapeit5/sse2neon.h | 981 | COMMENT | |
| LOW | recipes/shapeit5/sse2neon.h | 1101 | #endif | COMMENT |
| LOW | recipes/shapeit5/sse2neon.h | 1401 | // Compare the lower single-precision (32-bit) floating-point elements in a and | COMMENT |
| LOW | recipes/shapeit5/sse2neon.h | 1621 | COMMENT | |
| LOW | recipes/shapeit5/sse2neon.h | 1721 | COMMENT | |
| LOW | recipes/shapeit5/sse2neon.h | 1861 | vreinterpret_m64_s16(vset_lane_s16((b), vreinterpret_s16_m64(a), (imm))) | COMMENT |
| LOW | recipes/shapeit5/sse2neon.h | 2201 | // Compute the bitwise OR of packed single-precision (32-bit) floating-point | COMMENT |
| LOW | recipes/shapeit5/sse2neon.h | 2221 | // the lower element of dst. | COMMENT |
| LOW | recipes/shapeit5/sse2neon.h | 2241 | // values in dst. | COMMENT |
| LOW | recipes/shapeit5/sse2neon.h | 2301 | // b, then horizontally sum each consecutive 8 differences to produce four | COMMENT |
| LOW | recipes/shapeit5/sse2neon.h | 2321 | // Additional Netwon-Raphson iteration for accuracy | COMMENT |
| LOW | recipes/shapeit5/sse2neon.h | 2561 | _sse2neon_return(vreinterpret_m64_s16(ret));) | COMMENT |
| LOW | recipes/shapeit5/sse2neon.h | 2741 | // Store the lower single-precision (32-bit) floating-point element from a into | COMMENT |
| LOW | recipes/shapeit5/sse2neon.h | 2861 | #define _mm_ucomilt_ss _mm_comilt_ss | COMMENT |
| LOW | recipes/shapeit5/sse2neon.h | 2881 | COMMENT | |
| LOW | recipes/shapeit5/sse2neon.h | 3101 | COMMENT | |
| LOW | recipes/shapeit5/sse2neon.h | 3901 | // Convert packed signed 32-bit integers in a to packed double-precision | COMMENT |
| LOW | recipes/shapeit5/sse2neon.h | 4021 | #else | COMMENT |
| LOW | recipes/shapeit5/sse2neon.h | 4081 | #endif | COMMENT |
| LOW | recipes/shapeit5/sse2neon.h | 4121 | // element. | COMMENT |
| LOW | recipes/shapeit5/sse2neon.h | 4241 | // https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_extract_epi16 | COMMENT |
| LOW | recipes/shapeit5/sse2neon.h | 4261 | #if defined(__aarch64__) || defined(_M_ARM64) | COMMENT |
| LOW | recipes/shapeit5/sse2neon.h | 4561 | // of dst. | COMMENT |
| LOW | recipes/shapeit5/sse2neon.h | 4581 | COMMENT | |
| LOW | recipes/shapeit5/sse2neon.h | 4601 | // Merge the even lanes together with a 16-bit unsigned shift right + add. | COMMENT |
| LOW | recipes/shapeit5/sse2neon.h | 4621 | // \| \| | COMMENT |
| LOW | recipes/shapeit5/sse2neon.h | 4921 | // Set packed double-precision (64-bit) floating-point elements in dst with the | COMMENT |
| LOW | recipes/shapeit5/sse2neon.h | 5441 | // elements) from a into memory. mem_addr must be aligned on a 16-byte boundary | COMMENT |
| LOW | recipes/shapeit5/sse2neon.h | 5481 | COMMENT | |
| LOW | recipes/shapeit5/sse2neon.h | 5561 | COMMENT | |
| LOW | recipes/shapeit5/sse2neon.h | 5721 | #define _mm_ucomile_sd _mm_comile_sd | COMMENT |
| LOW | recipes/shapeit5/sse2neon.h | 5921 | // Alternatively add and subtract packed double-precision (64-bit) | COMMENT |
| LOW | recipes/shapeit5/sse2neon.h | 6021 | COMMENT | |
| LOW | recipes/shapeit5/sse2neon.h | 6801 | COMMENT | |
| LOW | recipes/shapeit5/sse2neon.h | 7081 | // https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_extract_epi64 | COMMENT |
| LOW | recipes/shapeit5/sse2neon.h | 7121 | return _mm_set_ps(floorf(f[3]), floorf(f[2]), floorf(f[1]), floorf(f[0])); | COMMENT |
| LOW | recipes/shapeit5/sse2neon.h | 7141 | { | COMMENT |
| LOW | recipes/shapeit5/sse2neon.h | 7161 | vsetq_lane_s64((b), vreinterpretq_s64_m128i(a), (imm))) | COMMENT |
| LOW | recipes/shapeit5/sse2neon.h | 7561 | // the rounding parameter, store the result as a double-precision floating-point | COMMENT |
| 539 more matches not shown… | ||||
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | recipes/diatracer/diatracer.py | 36 | CODE | |
| LOW | recipes/biotransformer/biotransformer.py | 41 | CODE | |
| LOW | recipes/mobster/mobster-to-vcf.py | 39 | CODE | |
| LOW | recipes/mobster/mobster.py | 39 | CODE | |
| LOW | recipes/biopet-vcfstats/biopet-vcfstats.py | 43 | CODE | |
| LOW | recipes/biopet-vcfstats/1.0/biopet-vcfstats.py | 43 | CODE | |
| LOW | recipes/biopet-vcfstats/1.1/biopet-vcfstats.py | 43 | CODE | |
| LOW | recipes/biopet-vcfstats/1.2/biopet-vcfstats.py | 43 | CODE | |
| LOW | recipes/vcf2genome/vcf2genome.py | 36 | CODE | |
| LOW | recipes/mpa-server/mpa-server.py | 51 | CODE | |
| LOW | recipes/mpa-server/mpa-server.py | 97 | CODE | |
| LOW | recipes/mpa-server/mpa-server.py | 116 | CODE | |
| LOW | recipes/mpa-server/mpa-server.py | 162 | CODE | |
| LOW | recipes/topas/topas.py | 36 | CODE | |
| LOW | recipes/biopet-basecounter/biopet-basecounter.py | 43 | CODE | |
| LOW | recipes/biopet-basecounter/0.1/biopet-basecounter.py | 43 | CODE | |
| LOW | recipes/mgf-formatter/mgf-formatter.py | 36 | CODE | |
| LOW | recipes/jmztab-m/jmztab-m.py | 42 | CODE | |
| LOW | recipes/biopet-sampleconfig/biopet-sampleconfig.py | 43 | CODE | |
| LOW | recipes/biopet-sampleconfig/0.2/biopet-sampleconfig.py | 43 | CODE | |
| LOW | recipes/figtree/figtree.py | 41 | CODE | |
| LOW | …pes/validate-fasta-database/validate-fasta-database.py | 39 | CODE | |
| LOW | …submission-tool-validator/submission-tool-validator.py | 41 | CODE | |
| LOW | recipes/cgview/cgview.py | 39 | CODE | |
| LOW | recipes/goenrichment/goenrichment.py | 41 | CODE | |
| LOW | recipes/hap-ibd/hap-ibd.py | 41 | CODE | |
| LOW | recipes/hops/MaltExtract.py | 36 | CODE | |
| LOW | recipes/hops/hops.py | 36 | CODE | |
| LOW | recipes/pepgenome/pepgenome.py | 38 | CODE | |
| LOW | recipes/examine/examine.py | 41 | CODE | |
| LOW | recipes/bioconda-repodata-patches/gen_patch_json.py | 88 | CODE | |
| LOW | recipes/sem/sem.py | 40 | CODE | |
| LOW | recipes/clinod/clinod.py | 39 | CODE | |
| LOW | recipes/biopet-seqstat/biopet-seqstat.py | 43 | CODE | |
| LOW | recipes/biopet-seqstat/1.0/biopet-seqstat.py | 43 | CODE | |
| LOW | recipes/biopet-seqstat/1.0.1/biopet-seqstat.py | 43 | CODE | |
| LOW | recipes/biopet-seqstat/0.1/biopet-seqstat.py | 43 | CODE | |
| LOW | recipes/haploview/haploview.py | 39 | CODE | |
| LOW | recipes/effectivet3/effectivet3.py | 39 | CODE | |
| LOW | recipes/dinosaur/dinosaur.py | 37 | CODE | |
| LOW | recipes/biopet-validatefastq/biopet-validatefastq.py | 43 | CODE | |
| LOW | recipes/clipandmerge/clipandmerge.py | 36 | CODE | |
| LOW | recipes/biopet-bamstats/biopet-bamstats.py | 43 | CODE | |
| LOW | recipes/biopet-bamstats/1.0/biopet-bamstats.py | 43 | CODE | |
| LOW | recipes/biopet-bamstats/1.0.1/biopet-bamstats.py | 43 | CODE | |
| LOW | …biopet-validateannotation/biopet-validateannotation.py | 43 | CODE | |
| LOW | recipes/msgf_plus/msgf_plus.py | 36 | CODE | |
| LOW | recipes/encyclopedia/encyclopedia.py | 41 | CODE | |
| LOW | recipes/damageprofiler/damageprofiler.py | 36 | CODE | |
| LOW | recipes/searchgui/searchgui.py | 40 | CODE | |
| LOW | recipes/snpeff/snpeff.py | 45 | CODE | |
| LOW | recipes/snpeff/5.1/snpeff.py | 41 | CODE | |
| LOW | recipes/snpeff/5.0/snpeff.py | 41 | CODE | |
| LOW | recipes/snpeff/5.1d/snpeff.py | 41 | CODE | |
| LOW | recipes/snpeff/4.3.1t/snpeff.py | 41 | CODE | |
| LOW | recipes/snpeff/4.5covid19/snpeff.py | 41 | CODE | |
| LOW | recipes/snpeff/5.2/snpeff.py | 45 | CODE | |
| LOW | recipes/jvarkit-msa2vcf/msa2vcf.py | 41 | CODE | |
| LOW | recipes/trimmomatic/trimmomatic.py | 40 | CODE | |
| LOW | recipes/trimmomatic/0.39/trimmomatic.py | 40 | CODE | |
| 73 more matches not shown… | ||||
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| MEDIUM | recipes/muset/build.sh | 13 | # Create the output directory | COMMENT |
| MEDIUM | recipes/genera/build.sh | 9 | # Define the Conda binary path | COMMENT |
| MEDIUM | recipes/ciri2/build.sh | 4 | # Create a binary directory in conda environment | COMMENT |
| MEDIUM | recipes/sqanti3/build.sh | 4 | # Define the isolated share directory for this specific version | COMMENT |
| MEDIUM | recipes/sqanti3/build.sh | 7 | # Create the necessary directories | COMMENT |
| MEDIUM | recipes/fungar/build.sh | 4 | # Create the bin directory for executable scripts | COMMENT |
| MEDIUM | recipes/fungar/build.sh | 7 | # Create the directory for the database | COMMENT |
| MEDIUM | recipes/sipros/build.sh | 37 | # Create the siproswf script | COMMENT |
| MEDIUM | recipes/sipros/build.sh | 44 | # Create the link of extractPro.sh | COMMENT |
| MEDIUM | recipes/wepp/build.sh | 71 | # Create the wrapper script | COMMENT |
| MEDIUM | recipes/bramble/build.sh | 24 | # Create a symbolic link so both `bramble` and `bramble-rs` work | COMMENT |
| MEDIUM | recipes/digest/build.sh | 54 | # Create the Python package directory if it doesn't exist | COMMENT |
| MEDIUM | recipes/ciri-full/build.sh | 9 | # Create a wrapper script to run the jar file | COMMENT |
| MEDIUM | recipes/longreadsum/build.sh | 14 | # Create the src directory | COMMENT |
| MEDIUM | recipes/clincnv/build.sh | 13 | # Define the wrapper script path | COMMENT |
| MEDIUM | recipes/clincnv/build.sh | 16 | # Create the wrapper script | COMMENT |
| MEDIUM | recipes/cats-rb/build.sh | 3 | #Creating the bin directory | COMMENT |
| MEDIUM | recipes/atlas-fastq-provider/build.sh | 6 | # Create a config if not already present | COMMENT |
| MEDIUM | recipes/tncomp_finder/build.sh | 3 | # Create the destination directory | COMMENT |
| MEDIUM | recipes/tncomp_finder/build.sh | 15 | # Create a wrapper script in bin | COMMENT |
| MEDIUM | recipes/metawepp/build.sh | 10 | # Create the wrapper script | COMMENT |
| MEDIUM | recipes/tn3_ta_finder/build.sh | 3 | # Create the destination directory | COMMENT |
| MEDIUM | recipes/tn3_ta_finder/build.sh | 15 | # Create a wrapper script in bin | COMMENT |
| MEDIUM | recipes/translatory/build.sh | 3 | # Create the binary directory in the Conda environment | COMMENT |
| MEDIUM | recipes/redundans/build.sh | 3 | #Define the install folder and binary folder and create them | COMMENT |
| MEDIUM | recipes/netmd/build.sh | 3 | # This file is part of the Karate Club package. | COMMENT |
| MEDIUM | recipes/cctyper/post-link.sh | 6 | ## Create a folder in the conda directory to host these files ("cct_data") | COMMENT |
| MEDIUM | recipes/gzrt/build.sh | 27 | # Create a temporary directory | COMMENT |
| MEDIUM | recipes/gzrt/build.sh | 30 | # Create a symlink named cc that points to $CC | COMMENT |
| MEDIUM | recipes/unifire/build.sh | 67 | # Create a wrapper to invoke it with python | COMMENT |
| MEDIUM | recipes/absense/build.sh | 12 | # Define the Conda binary path | COMMENT |
| MEDIUM⚡ | recipes/corona_lineage_dynamics/build.sh | 5 | # Define the target directory | COMMENT |
| MEDIUM⚡ | recipes/corona_lineage_dynamics/build.sh | 8 | # Create the target directory | COMMENT |
| MEDIUM⚡ | recipes/corona_lineage_dynamics/build.sh | 14 | # Create the proxy script in $PREFIX/bin | COMMENT |
| MEDIUM | recipes/jacusa2/build.sh | 3 | # Create the installation directory | COMMENT |
| MEDIUM | recipes/jacusa2/build.sh | 9 | # Create a wrapper script named "JACUSA2" so users can run the jar directly | COMMENT |
| MEDIUM | recipes/neptune-signature/post-link.sh | 15 | # Creating a new executable (while preserving permissions). The new executable | COMMENT |
| MEDIUM | recipes/acedrg/build.sh | 24 | # Create a symlink for libmol if the upstream build installs it under libexec | COMMENT |
| MEDIUM | recipes/pybigtools/build.sh | 26 | # Creating the sdist from the monorepo placed pyproject.toml one level above Cargo.toml. | COMMENT |
| MEDIUM | recipes/cats-rf/build.sh | 3 | #Creating the bin directory | COMMENT |
| MEDIUM | recipes/haplink/build.sh | 33 | # Create a permanent depot | COMMENT |
| MEDIUM | recipes/hifiadapterfilt/build.sh | 14 | # Create an activation script for Bioconda | COMMENT |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| MEDIUM | recipes/altair-mf/meta.yaml | 3 | # ------------------------------------------------ | COMMENT |
| MEDIUM | recipes/ltr_retriever/build.sh | 10 | # ----------------- | COMMENT |
| MEDIUM | recipes/ltr_retriever/build.sh | 21 | # ----------------- | COMMENT |
| MEDIUM⚡ | recipes/phageflow/meta.yaml | 34 | # ── QC ─────────────────────────────────────────────────────────────────── | COMMENT |
| MEDIUM⚡ | recipes/phageflow/meta.yaml | 38 | # ── Host removal ───────────────────────────────────────────────────────── | COMMENT |
| MEDIUM⚡ | recipes/phageflow/meta.yaml | 44 | # ── Assembly ───────────────────────────────────────────────────────────── | COMMENT |
| MEDIUM⚡ | recipes/phageflow/meta.yaml | 48 | # ── Coverage ───────────────────────────────────────────────────────────── | COMMENT |
| MEDIUM⚡ | recipes/phageflow/meta.yaml | 50 | # ── Viral ID ───────────────────────────────────────────────────────────── | COMMENT |
| MEDIUM⚡ | recipes/phageflow/meta.yaml | 52 | # ── Quality ────────────────────────────────────────────────────────────── | COMMENT |
| MEDIUM⚡ | recipes/phageflow/meta.yaml | 57 | # ── Annotation ─────────────────────────────────────────────────────────── | COMMENT |
| MEDIUM | recipes/themis/build.sh | 11 | # ----------------------------------------------------------------------------- | COMMENT |
| MEDIUM | recipes/themis/build.sh | 26 | # ----------------------------------------------------------------------------- | COMMENT |
| MEDIUM⚡ | recipes/themis/build.sh | 41 | # ----------------------------------------------------------------------------- | COMMENT |
| MEDIUM⚡ | recipes/themis/build.sh | 48 | # ----------------------------------------------------------------------------- | COMMENT |
| MEDIUM⚡ | recipes/themis/build.sh | 49 | # ----------------------------------------------------------------------------- | COMMENT |
| MEDIUM⚡ | recipes/themis/build.sh | 51 | # ----------------------------------------------------------------------------- | COMMENT |
| MEDIUM⚡ | recipes/themis/build.sh | 52 | # ----------------------------------------------------------------------------- | COMMENT |
| MEDIUM | recipes/csem/build.sh | 4 | # -------------------------------------------------------------------------- | COMMENT |
| MEDIUM | recipes/csem/build.sh | 13 | # -------------------------------------------------------------------------- | COMMENT |
| MEDIUM | recipes/unifire/post-link.sh | 18 | # ------------------------------------------------------------ | COMMENT |
| MEDIUM | recipes/unifire/post-link.sh | 20 | # ------------------------------------------------------------ | COMMENT |
| MEDIUM⚡ | recipes/unifire/post-link.sh | 37 | # ------------------------------------------------------------ | COMMENT |
| MEDIUM⚡ | recipes/unifire/post-link.sh | 39 | # ------------------------------------------------------------ | COMMENT |
| MEDIUM⚡ | recipes/unifire/post-link.sh | 44 | # ------------------------------------------------------------ | COMMENT |
| MEDIUM⚡ | recipes/unifire/post-link.sh | 46 | # ------------------------------------------------------------ | COMMENT |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | recipes/sfold/meta.yaml | 30 | - sfold -h # Check if sfold command runs successfully | CODE |
| LOW | recipes/qualimap/build.sh | 13 | # Set QUALIMAP_HOME to libraries path. This can help qualimap know where scripts/ forlder is. | COMMENT |
| LOW | recipes/qualimap/build.sh | 15 | # Set classpath to libraries | COMMENT |
| LOW | recipes/qualimap/2.1.1/build.sh | 13 | # Set QUALIMAP_HOME to libraries path. This can help qualimap know where scripts/ forlder is. | COMMENT |
| LOW | recipes/qualimap/2.1.1/build.sh | 15 | # Set classpath to libraries | COMMENT |
| LOW | recipes/qualimap/2.2.2c/build.sh | 13 | # Set QUALIMAP_HOME to libraries path. This can help qualimap know where scripts/ forlder is. | COMMENT |
| LOW | recipes/qualimap/2.2.2c/build.sh | 15 | # Set classpath to libraries | COMMENT |
| LOW | recipes/gtdbtk/download-db.sh | 47 | # Check if this is overriding an existing version | COMMENT |
| LOW | recipes/b2btools/.run_test.sh | 47 | # Check if the status code is non-zero and exit with an error code | COMMENT |
| LOW | recipes/b2btools/.run_test.sh | 61 | # Check if the file is a CSV and has more than one row | COMMENT |
| LOW | recipes/b2btools/.run_test.sh | 90 | # Check if the status code is non-zero and exit with an error code | COMMENT |
| LOW | recipes/b2btools/.run_test.sh | 104 | # Check if the file is a CSV and has more than one row | COMMENT |
| LOW | recipes/b2btools/.run_test.sh | 133 | # Check if the status code is non-zero and exit with an error code | COMMENT |
| LOW | recipes/b2btools/.run_test.sh | 147 | # Check if the file is a CSV and has more than one row | COMMENT |
| LOW | recipes/b2btools/.run_test.sh | 182 | # Check if the status code is non-zero and exit with an error code | COMMENT |
| LOW | recipes/b2btools/.run_test.sh | 196 | # Check if the file is a CSV and has more than one row | COMMENT |
| LOW | recipes/b2btools/.run_test.sh | 229 | # Check if the status code is non-zero and exit with an error code | COMMENT |
| LOW | recipes/b2btools/.run_test.sh | 243 | # Check if the file is a CSV and has more than one row | COMMENT |
| LOW | recipes/b2btools/.run_test.sh | 274 | # Check if the status code is non-zero and exit with an error code | COMMENT |
| LOW | recipes/b2btools/.run_test.sh | 288 | # Check if the file is a CSV and has more than one row | COMMENT |
| LOW | recipes/mango/post-link.sh | 3 | # Set SPARK_HOME to conda installed pyspark package if not already set | COMMENT |
| LOW | recipes/mango/activate.sh | 3 | # Set SPARK_HOME to conda installed pyspark package if not already set | COMMENT |
| LOW | recipes/earlgrey/build.sh | 47 | # Set permissions to files | COMMENT |
| LOW | recipes/pyopenms/build.sh | 24 | # Set INSTALL_RPATH to PREFIX such that there are no warnings during linkage fixing of conda-build | COMMENT |
| LOW | recipes/minimac4/build.sh | 6 | # Set CXXFLAGS to include the correct path to lzma.h and LDFLAGS to include the path to liblzma | COMMENT |
| LOW | recipes/haddock_biobb/post-link.sh | 3 | # Check if gcc is available. As gcc is hardcoded in haddock3 setup.py, it's unavailable on Bioconda tests. | COMMENT |
| LOW | recipes/openms-meta/build.sh | 24 | # Set INSTALL_RPATH to PREFIX such that there are no warnings during linkage fixing of conda-build | COMMENT |
| LOW | scripts/check-for-additional-platforms.sh | 45 | # Check if any additional platforms match this job | COMMENT |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | recipes/biotransformer/biotransformer.py | 12 | CODE | |
| LOW | recipes/crisper_recognition_tool/crt.py | 12 | CODE | |
| LOW | recipes/pyopt/run_test.py | 2 | CODE | |
| LOW | recipes/pyopt/run_test.py | 3 | CODE | |
| LOW | recipes/pyopt/run_test.py | 4 | CODE | |
| LOW | recipes/pyopt/run_test.py | 5 | CODE | |
| LOW | recipes/pyopt/run_test.py | 6 | CODE | |
| LOW | recipes/pyopt/run_test.py | 7 | CODE | |
| LOW | recipes/pyopt/run_test.py | 8 | CODE | |
| LOW | recipes/pyopt/run_test.py | 9 | CODE | |
| LOW | recipes/pyopt/run_test.py | 10 | CODE | |
| LOW | recipes/pyopt/run_test.py | 11 | CODE | |
| LOW | recipes/pyopt/run_test.py | 12 | CODE | |
| LOW | recipes/pyopt/run_test.py | 13 | CODE | |
| LOW | recipes/pyopt/run_test.py | 14 | CODE | |
| LOW | recipes/bioconda-repodata-patches/gen_patch_json.py | 3 | CODE | |
| LOW | recipes/bioconda-repodata-patches/gen_patch_json.py | 3 | CODE | |
| LOW | recipes/bioconda-repodata-patches/gen_patch_json.py | 3 | CODE | |
| LOW | recipes/np-likeness-scorer/np-likeness.py | 12 | CODE | |
| LOW | recipes/transabyss/setup.py | 1 | CODE | |
| LOW | recipes/transabyss/setup.py | 2 | CODE | |
| LOW | recipes/transabyss/setup.py | 2 | CODE | |
| LOW | recipes/mango/run_test.py | 2 | CODE | |
| LOW | recipes/mango/run_test.py | 3 | CODE | |
| LOW | recipes/mango/run_test.py | 4 | CODE | |
| LOW | recipes/mango/run_test.py | 5 | CODE | |
| LOW | recipes/mango/run_test.py | 6 | CODE | |
| LOW | recipes/fseq/fseq.py | 14 | CODE | |
| LOW | recipes/fseq/fseq.py | 18 | CODE | |
| LOW | …cipes/jvarkit-wgscoverageplotter/wgscoverageplotter.py | 12 | CODE | |
| LOW | recipes/pysam/run_test.py | 1 | CODE | |
| LOW | recipes/gemoma/GeMoMa.py | 12 | CODE | |
| LOW | recipes/bamr/run_test.py | 1 | CODE |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | recipes/cactus/build.sh | 45 | # cactus-gfa-tools is required but doesn't have tags. They just use exact commits in their scripts | COMMENT |
| MEDIUM | recipes/bioconductor-visiumstitched/meta.yaml | 80 | description: This package provides helper functions for working with multiple Visium capture areas that overlap each o | CODE |
| MEDIUM | recipes/r-genekitr/meta.yaml | 95 | # Description: Provides features for searching, converting, analyzing, plotting, and exporting data effortlessly by inpu | COMMENT |
| MEDIUM | recipes/delve-bio/meta.yaml | 9 | url: https://github.com/berndbohmeier/delve/archive/v{{ version }}.tar.gz | CODE |
| MEDIUM | recipes/delve-bio/meta.yaml | 34 | home: https://github.com/berndbohmeier/delve | CODE |
| MEDIUM | recipes/bwa-mem3/build.sh | 80 | # bundled MI_OVERRIDE=ON libmimalloc.a is the only robust override on Linux, | COMMENT |
| MEDIUM | recipes/tapestry/meta.yaml | 8 | url: https://github.com/johnomics/tapestry/archive/v{{ version}}.tar.gz | CODE |
| MEDIUM | recipes/tapestry/meta.yaml | 38 | home: https://github.com/johnomics/tapestry | CODE |
| MEDIUM | recipes/tapestry/meta.yaml | 43 | dev_url: https://github.com/johnomics/tapestry | CODE |
| MEDIUM | recipes/enzywizard-energy/meta.yaml | 41 | # OpenMM can leverage CUDA if available in the environment. | COMMENT |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| MEDIUM | recipes/bioconductor-breakpointrdata/meta.yaml | 36 | summary: Strand-seq data for demonstration purposes | CODE |
| LOW | recipes/mccortex/run_test.sh | 9 | # let's make sure to check both k-mer sizes were compiled | COMMENT |
| MEDIUM | recipes/bioconductor-aneufinderdata/meta.yaml | 35 | summary: WGSCS Data for Demonstration Purposes | CODE |
| MEDIUM | recipes/bioconductor-aneufinderdata/meta.yaml | 36 | description: Whole-genome single cell sequencing data for demonstration purposes in the AneuFinder package. | CODE |
| MEDIUM | recipes/bioconductor-targetsearchdata/meta.yaml | 36 | description: Example files of GC-MS data for the TargetSearch Package. The package contains raw NetCDF files from a E. | CODE |
| MEDIUM | recipes/bioconductor-chromstardata/meta.yaml | 35 | summary: ChIP-seq data for Demonstration Purposes | CODE |
| MEDIUM | recipes/bioconductor-chromstardata/meta.yaml | 36 | description: ChIP-seq data for demonstration purposes in the chromstaR package. | CODE |
| MEDIUM | recipes/bioconductor-prebsdata/meta.yaml | 36 | description: 'This package contains data required to run examples in ''prebs'' package. The data files include: 1) Sma | CODE |
| LOW | recipes/optitype/config.ini | 11 | # environment OptiType is run, so make sure to include it in PATH. | COMMENT |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | recipes/mpa-server/mpa-server.py | 198 | def prompt_user_for_data_download(): | CODE |
| LOW | recipes/needletail/run_test.py | 22 | def test_can_parse_fasta_file(self): | CODE |
| LOW | recipes/needletail/run_test.py | 41 | def test_can_parse_fastq_file(self): | CODE |
| LOW | recipes/pycoverm/run_test.py | 17 | def test_get_coverages_from_bam(self): | CODE |
| LOW | recipes/bioconda-repodata-patches/gen_patch_json.py | 53 | def _gen_patch_instructions_per_key(index_per_key, new_index, subdir): | CODE |
| LOW | recipes/bioconda-repodata-patches/show_diff.py | 21 | def show_record_diffs_per_key(packages_key, subdir, ref_repodata, new_repodata): | CODE |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| MEDIUM | recipes/ena-webin-cli/ena_webin_cli.py | 122 | print(f"Error: failed to exec java: {e}", file=sys.stderr) | CODE |
| LOW | recipes/ega-cryptor/ega-cryptor.py | 106 | except Exception as e: | CODE |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| MEDIUM | recipes/enzywizard-batch/meta.yaml | 52 | # Note: This is a meta-workflow tool that orchestrates many EnzyWizard components. | COMMENT |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | recipes/verifybamid2/verifybamid2.sh | 5 | # Usage: | COMMENT |